Add tbl_proportion() and proportion comparison verbs

[Melkiades]

Adds a reusable stats layer for binary/response summary tables (RSPT01), so templates hold only cosmetics.

Three verbs, statistics and tabulation separated from wording:

• Added tbl_proportion() to summarize a binary or multinomial variable as proportions with confidence intervals (estimate and CI on separate rows), with a selectable CI method and conf.level. (Add tbl_proportion() and proportion comparison verbs #303)

• Added add_proportion_difference() to append the difference in rates, its confidence interval, and a p-value ("chisq", "fisher", or "cmh"), with stratified (Cochran-Mantel-Haenszel) support via strata. (Add tbl_proportion() and proportion comparison verbs #303)

• Added add_proportion_odds_ratio() to append an odds ratio, with stratified (Cochran-Mantel-Haenszel) support via strata. (Add tbl_proportion() and proportion comparison verbs #303)

CI method and level match cardx::ard_categorical_ci(); the difference CI and p-value are verified against prop.test(), and the odds ratio against a manual 2x2.

Fixes #303

[github-actions]

Unit Tests Summary

  1 files  324 suites   1m 50s ⏱️
324 tests 324 ✅ 0 💤 0 ❌
938 runs  938 ✅ 0 💤 0 ❌

Results for commit 4324432.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
tbl_proportion	👶		$+0.00$	$+5$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
tbl_baseline_chg	💚	$12.68$	$-1.34$	tbl_baseline_chg_works
tbl_hierarchical_rate_and_count	💚	$9.87$	$-1.26$	tbl_hierarchical_rate_and_count_works
tbl_hierarchical_rate_by_grade	💚	$11.22$	$-1.78$	tbl_hierarchical_rate_by_grade_works
tbl_proportion	👶		$+0.00$	add_proportion_difference_adds_the_comparison_block
tbl_proportion	👶		$+0.00$	add_proportion_difference_supports_fisher_and_cmh
tbl_proportion	👶		$+0.00$	add_proportion_odds_ratio_adds_an_odds_ratio_row
tbl_proportion	👶		$+0.00$	informative_errors_are_raised
tbl_proportion	👶		$+0.00$	odds_ratio_matches_the_2x2_hand_calculation
tbl_proportion	👶		$+0.00$	stratified_odds_ratio_uses_the_CMH_common_odds_ratio
tbl_proportion	👶		$+3.06$	tbl_proportion_binary_summary_works
tbl_proportion	👶		$+0.00$	tbl_proportion_multinomial_summary_preserves_factor_level_order
tbl_proportion	👶		$+0.01$	tbl_proportion_supports_different_CI_methods_and_conf.level
tbl_proportion	👶		$+0.00$	tbl_proportion_works_without_a_by_variable
tbl_rmpt	💚	$6.70$	$-2.01$	tbl_rmpt_works_with_default_parameters_Example_1_
tbl_shift	💚	$3.86$	$-1.81$	tbl_shift_strata_location_
tbl_survfit_quantiles	💔	$0.18$	$+1.57$	tbl_survfit_quantiles_works
tbl_survfit_times	💚	$1.92$	$-1.69$	tbl_survfit_times_works
tbl_with_pools	💔	$5.75$	$+1.17$	tbl_with_pools_validates_inputs_correctly

Results for commit f61892d

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------
R/add_blank_rows.R                          63       0  100.00%
R/add_difference_row.R                     101       0  100.00%
R/add_forest_utils.R                        97      10  89.69%   76-79, 94-100
R/add_forest.R                             139       0  100.00%
R/add_hierarchical_count_row.R              33       0  100.00%
R/add_label_column.R                        26       0  100.00%
R/add_proportion_difference.R              150       1  99.33%   245
R/add_proportion_odds_ratio.R               57       0  100.00%
R/adjust_stat_columns_wrap.R                29       1  96.55%   59
R/annotate_gg_km.R                         141       0  100.00%
R/annotate_gg_pkc.R                        100       0  100.00%
R/annotate_gg.R                             94       0  100.00%
R/ard_tabulate_abnormal_by_baseline.R       65       0  100.00%
R/crane-package.R                            2       2  0.00%    26-27
R/deprecated.R                              21      21  0.00%    18-54
R/df_add_poolings.R                         41       0  100.00%
R/get_cox_pairwise_df.R                    163       0  100.00%
R/gg_km_utils.R                             39      14  64.10%   20-37
R/gg_km.R                                  143      37  74.13%   55-58, 75, 102, 176-181, 184-187, 197-199, 204-205, 239-241, 248-251, 255, 266-270, 283, 285-287
R/gg_lineplot.R                            121       0  100.00%
R/gg_mmrm_lineplot.R                       102       1  99.02%   106
R/gg_pkc_lineplot.R                         98       0  100.00%
R/gg_utils.R                               222       0  100.00%
R/label_roche.R                             72       0  100.00%
R/modify_header_rm_md.R                     18       2  88.89%   35-36
R/modify_split_caption.R                    26       0  100.00%
R/modify_zero_recode.R                      20       1  95.00%   64
R/pk_helper.R                              499       0  100.00%
R/reverse_difference_ci.R                   33       0  100.00%
R/tbl_baseline_chg.R                       188       0  100.00%
R/tbl_coxph.R                               90       1  98.89%   229
R/tbl_hierarchical_incidence_rate.R        291       4  98.63%   430-433
R/tbl_hierarchical_rate_and_count.R        339      13  96.17%   343, 425, 446-456
R/tbl_hierarchical_rate_by_grade.R         317       3  99.05%   169-171
R/tbl_listing.R                             36       0  100.00%
R/tbl_mmrm.R                               344       6  98.26%   452-456, 548
R/tbl_null_report.R                         10       0  100.00%
R/tbl_proportion.R                         141      13  90.78%   100-103, 107-111, 114-117
R/tbl_rmpt.R                               157      12  92.36%   299-304, 316-321
R/tbl_roche_subgroups.R                    157       0  100.00%
R/tbl_roche_summary.R                       64       0  100.00%
R/tbl_shift.R                              111       0  100.00%
R/tbl_survfit_quantiles.R                  154       0  100.00%
R/tbl_survfit_times.R                       92       0  100.00%
R/tbl_with_pools.R                          79       1  98.73%   317
R/theme_gtsummary_roche.R                   87       1  98.85%   61
R/utils.R                                   42       0  100.00%
TOTAL                                     5414     144  97.34%

Diff against main

Filename                         Stmts    Miss  Cover
-----------------------------  -------  ------  --------
R/add_proportion_difference.R     +150      +1  +99.33%
R/add_proportion_odds_ratio.R      +57       0  +100.00%
R/tbl_proportion.R                +141     +13  +90.78%
TOTAL                             +348     +14  -0.09%

Results for commit: 4324432

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[wzfrank]

We need to add an argument to customize Wald, with continuity correction.

[Melkiades]

Addressed in 4324432c. The default CI row label for the continuity-corrected methods (waldcc, wilsoncc, strat_wilsoncc) now reads "Wald, with continuity correction" (previously "Wald, with correction"), matching the statistical meaning of the cc suffix. The label was already overridable via the ci_label argument on both tbl_proportion() and add_proportion_difference(); this change corrects the default wording. Docs, snapshot, and NEWS updated.

[wzfrank]

Thanks I think this looks good now!