1444/1445: Two more CMH prop diff (test) methods by danielinteractive · Pull Request #1454 · insightsengineering/tern

danielinteractive · 2025-12-11T07:48:02Z

closes #1444 and #1445

…ghtsengineering/tern into 1444_1445_prop_diff_methods

github-actions · 2025-12-11T08:05:54Z

Unit Tests Summary

1 files 85 suites 1m 46s ⏱️
898 tests 889 ✅ 9 💤 0 ❌
2 219 runs 1 510 ✅ 709 💤 0 ❌

Results for commit 5f20cd2.

♻️ This comment has been updated with latest results.

github-actions · 2025-12-11T08:05:59Z

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	$±Time$	Test Case
prop_diff	👶	$+0.04$	h_miettinen_nurminen_var_est_works_as_expected
prop_diff	👶	$+0.03$	prop_diff_cmh_works_correctly_with_Miettinen_Nurminen_variance_estimator
prop_diff	👶	$+0.04$	s_proportion_diff_works_with_CMH_Miettinen_and_Nurminen_method
test_proportion_diff	👶	$+0.04$	prop_cmh_with_Wilson_Hilferty_transformation_works
test_proportion_diff	👶	$+0.09$	test_proportion_diff_edge_case_all_responder_by_CMH_with_Wilson_Hilferty_transformation

Results for commit 0a32d59

♻️ This comment has been updated with latest results.

shajoezhu · 2025-12-11T08:13:01Z

checking downstream at insightsengineering/scda.test#204 and https://github.com/insightsengineering/tern/actions/runs/20126364807

tests/testthat/test-test_proportion_diff.R

github-actions · 2025-12-11T09:20:48Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                     101       3  97.03%   242, 244-245
R/abnormal_by_marked.R                        88       8  90.91%   94-98, 281, 283-284
R/abnormal_by_worst_grade.R                   94       3  96.81%   215, 217-218
R/abnormal_lab_worsen_by_baseline.R          159      10  93.71%   205-208, 213, 215-216, 459-461
R/abnormal.R                                  78       2  97.44%   222, 224
R/analyze_variables.R                        295       5  98.31%   593-596, 789
R/analyze_vars_in_cols.R                     178      14  92.13%   178, 221, 235-236, 238, 246-254
R/bland_altman.R                              92       1  98.91%   46
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                         35       0  100.00%
R/control_incidence_rate.R                    10       0  100.00%
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                         115       4  96.52%   74, 270-271, 273
R/count_missed_doses.R                        89       4  95.51%   206-209
R/count_occurrences_by_grade.R               169       8  95.27%   178, 386, 388, 465, 467, 469, 473-474
R/count_occurrences.R                        137      10  92.70%   119, 262-264, 330-332, 334, 338-339
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 73       2  97.26%   220, 223
R/count_patients_with_flags.R                 93       2  97.85%   234, 236
R/count_values.R                              61       2  96.72%   193, 196
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 238, 253, 261, 267-268
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            113       0  100.00%
R/desctools_binom_diff.R                     621      64  89.69%   53, 88-89, 125-126, 129, 199, 223-232, 264, 266, 286, 290, 294, 298, 353, 356, 359, 362, 422, 430, 439, 444-447, 454, 457, 466, 469, 516-517, 519-520, 522-523, 525-526, 593, 604-616, 620, 663, 676, 680
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  86       4  95.35%   65, 212, 214-215
R/estimate_proportion.R                      240       7  97.08%   88, 99, 255, 257-258, 389, 553
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     183       2  98.91%   141, 276
R/g_forest.R                                 585      60  89.74%   240, 252-255, 260-261, 275, 277, 287-290, 335-338, 345, 414, 501, 514, 518-519, 524-525, 538, 554, 601, 630, 705, 714, 720, 739, 794-814, 817, 828, 847, 902, 905, 1040-1045
R/g_ipp.R                                    133       0  100.00%
R/g_km.R                                     350      57  83.71%   285-288, 307-309, 363-366, 400, 428, 432-475, 482-486
R/g_lineplot.R                               261      22  91.57%   222, 397-404, 443-453, 562, 570
R/g_step.R                                    68       1  98.53%   108
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        73       0  100.00%
R/h_biomarkers_subgroups.R                    91      23  74.73%   40-42, 84-103
R/h_cox_regression.R                         110       0  100.00%
R/h_incidence_rate.R                          45       0  100.00%
R/h_km.R                                     509      41  91.94%   137, 189-194, 287, 378, 380-381, 392-394, 413, 420-421, 423-425, 433-435, 460, 465-468, 651-654, 1108-1119
R/h_logistic_regression.R                    468       3  99.36%   203-204, 273
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           77      12  84.42%   50-55, 107-112
R/h_response_subgroups.R                     178      18  89.89%   257-270, 329-334
R/h_stack_by_baskets.R                        64       1  98.44%   89
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           73       6  91.78%   111-116
R/h_survival_duration_subgroups.R            207      18  91.30%   259-271, 336-341
R/imputation_rule.R                           17       0  100.00%
R/incidence_rate.R                           103       7  93.20%   68-73, 242
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              26       5  80.77%   39, 62-63, 96, 106
R/odds_ratio.R                               157       4  97.45%   270-273
R/prop_diff_test.R                           174       2  98.85%   264, 266
R/prop_diff.R                                382      18  95.29%   92-96, 128, 323, 325, 411-418, 566, 839
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R            124      10  91.94%   88-91, 270-275
R/response_subgroups.R                       252      16  93.65%   100-105, 271-275, 280, 282-283, 310-311
R/riskdiff.R                                  65       4  93.85%   94-97
R/rtables_access.R                            38       0  100.00%
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       0  100.00%
R/summarize_ancova.R                         150       2  98.67%   327-328
R/summarize_change.R                          72       3  95.83%   175, 177-178
R/summarize_colvars.R                         13       1  92.31%   75
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      269      10  96.28%   129-130, 202-203, 459-463, 596
R/summarize_num_patients.R                   121      10  91.74%   122-124, 244, 248, 252-253, 337-338, 340
R/summarize_patients_exposure_in_cols.R      155       7  95.48%   58, 232-233, 237, 357-358, 362
R/survival_biomarkers_subgroups.R            136      10  92.65%   117-122, 228-231
R/survival_coxph_pairwise.R                  124       5  95.97%   52-53, 248, 250-251
R/survival_duration_subgroups.R              250      15  94.00%   124-129, 268-273, 286, 288-289
R/survival_time.R                            120       1  99.17%   251
R/survival_timepoint.R                       153       2  98.69%   320, 322
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       196       0  100.00%
R/utils_factor.R                              87       1  98.85%   99
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            125       9  92.80%   39, 46, 414-415, 537-541
R/utils_split_funs.R                          52       2  96.15%   82, 94
R/utils.R                                    141       7  95.04%   131, 134, 137, 141, 150-151, 345
TOTAL                                      12074     583  95.17%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/prop_diff_test.R      +15       0  +0.11%
R/prop_diff.R           +50       0  +0.71%
TOTAL                   +65       0  +0.03%

Results for commit: 5f20cd2

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

shajoezhu

lgtm! thanks @danielinteractive https://github.com/insightsengineering/tern/actions/runs/20128497426 lgtm!
insightsengineering/scda.test#204

danielinteractive and others added 6 commits December 11, 2025 13:14

merge in wilson-hilferty stuff

2b98f78

Add cmh_mn method for prop diff CI/SE

16592bd

[skip style] [skip vbump] Restyle files

116df22

better documentation for helper

f6641b0

Merge branch '1444_1445_prop_diff_methods' of https://github.com/insi…

8857711

…ghtsengineering/tern into 1444_1445_prop_diff_methods

[skip style] [skip vbump] Restyle files

4d60898

Trigger Build

f25cf39

shajoezhu reviewed Dec 11, 2025

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tests/testthat/test-test_proportion_diff.R Show resolved Hide resolved

danielinteractive added 2 commits December 11, 2025 16:52

fix check note with pkg prefix

a5e7b00

add snapshot again

5f20cd2

shajoezhu approved these changes Dec 11, 2025

View reviewed changes

danielinteractive merged commit 3de8496 into main Dec 11, 2025
34 checks passed

danielinteractive deleted the 1444_1445_prop_diff_methods branch December 11, 2025 12:17

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1444/1445: Two more CMH prop diff (test) methods#1454

1444/1445: Two more CMH prop diff (test) methods#1454
danielinteractive merged 9 commits intomainfrom
1444_1445_prop_diff_methods

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