Refactor remaining analysis functions

[edelarua]

Pull Request

Fixes #1397

[github-actions]

Unit Tests Summary

    1 files     85 suites   1m 16s ⏱️
  879 tests   870 ✅   9 💤 0 ❌
1 894 runs  1 196 ✅ 698 💤 0 ❌

Results for commit 6b5313c.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
analyze_vars_in_cols	💔	$2.55$	$+3.03$	$+17$	$-7$	$0$	$0$
count_occurrences	💔	$0.78$	$+1.58$	$+10$	$-8$	$0$	$0$
summarize_coxreg	💔	$3.43$	$+1.64$	$+13$	$-13$	$0$	$0$
summarize_num_patients	💔	$1.18$	$+1.08$	$+18$	$-16$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
analyze_vars_in_cols	💔	$0.50$	$+1.45$	summarize_works_with_nested_analyze

Results for commit 749621b

♻️ This comment has been updated with latest results.

[github-actions]

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                        287       5  98.26%   587-590, 778
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                          59       1  98.31%   74
R/count_missed_doses.R                        36       0  100.00%
R/count_occurrences_by_grade.R               163       5  96.93%   178, 386, 388, 465, 467
R/count_occurrences.R                        131       8  93.89%   119, 262-264, 330-333
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                      229       7  96.94%   84, 95, 234, 236-237, 368, 534
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                               260      22  91.54%   204, 378-385, 424-434, 543, 551
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                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               157       4  97.45%   270-273
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      15  94.34%   70-73, 105, 290-297, 440, 605
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                       247      16  93.52%   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                         142       2  98.59%   316-317
R/summarize_change.R                          71       3  95.77%   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                   115       9  92.17%   122-124, 244-245, 247, 329-330, 332
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              245      15  93.88%   124-129, 268-273, 286, 288-289
R/survival_time.R                            120       1  99.17%   251
R/survival_timepoint.R                       153       2  98.69%   302, 304
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       178       0  100.00%
R/utils_factor.R                              87       1  98.85%   84
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, 405-406, 528-532
R/utils_split_funs.R                          52       2  96.15%   82, 94
R/utils.R                                    141       7  95.04%   118, 121, 124, 128, 137-138, 332
TOTAL                                      11685     563  95.18%

Diff against main

Filename                                   Stmts    Miss  Cover
---------------------------------------  -------  ------  -------
R/abnormal_by_baseline.R                      +2       0  +0.06%
R/abnormal_by_marked.R                        +2       0  +0.21%
R/abnormal_by_worst_grade.R                   +2       0  +0.07%
R/abnormal_lab_worsen_by_baseline.R           +2       0  +0.08%
R/abnormal.R                                  +2       0  +0.07%
R/count_occurrences_by_grade.R               +10      +3  -1.76%
R/count_occurrences.R                        +16      +7  -5.24%
R/count_patients_with_event.R                +12      +1  -1.10%
R/count_patients_with_flags.R                 +9      +1  -0.96%
R/count_values.R                              -7       0  -0.34%
R/incidence_rate.R                           +17       0  +1.34%
R/response_subgroups.R                        +1       0  +0.03%
R/riskdiff.R                                   0      -1  +1.54%
R/summarize_change.R                          -2      +2  -2.86%
R/summarize_colvars.R                         +3      +1  -7.69%
R/summarize_num_patients.R                   +22      +5  -3.53%
R/summarize_patients_exposure_in_cols.R      +59      +6  -3.47%
R/survival_duration_subgroups.R               +1       0  +0.03%
R/survival_time.R                             +9      +1  -0.83%
TOTAL                                       +160     +26  -0.16%

Results for commit: 6b5313c

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[edelarua]

@Melkiades I refactored summarize_num_patients() which is part of your batch 1 issue since it uses afun_riskdiff - if you've already worked on this one (or just want to copy my changes to your PR) and want me to revert my changes here let me know!! Otherwise I'll just leave it here.

[edelarua]

@Melkiades I made all of the changes that you suggested so this should be ready for another review when you get a chance :)

[Melkiades]

Lgtm!!! Thanks Emily!! :))

[shajoezhu]

thanks so much guys! @edelarua @Melkiades