713 summarize_occurrences_by_grade missing numeric grades bug

[edelarua]

Closes #713

[github-actions]

Unit Tests Summary

       1 files     115 suites   2m 20s ⏱️
   792 tests    792 ✔️ 0 💤 0 ❌
1 195 runs  1 195 ✔️ 0 💤 0 ❌

Results for commit aa73537.

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   124-128
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   205-207
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        138       3  97.83%   135, 247, 266
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                          47       1  97.87%   52
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       3  96.43%   148, 163-164
R/count_occurrences.R                         61       1  98.36%   89
R/count_patients_events_in_cols.R             67       0  100.00%
R/count_patients_with_event.R                 72      22  69.44%   206-229
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           318       0  100.00%
R/coxph.R                                    168     121  27.98%   19-50, 217-445
R/d_pkparam.R                                405       0  100.00%
R/decorate_grob.R                            167     167  0.00%    158-517
R/desctools_binom_diff.R                     668     415  37.87%   60, 65, 87-97, 100-101, 122-137, 140-179, 182-189, 199-247, 250-261, 264-276, 279-292, 300, 302, 322, 326, 330, 334, 370, 386, 389, 392, 395, 402, 417-419, 422-425, 435-442, 445-452, 455-456, 458-461, 463-464, 466-467, 471-477, 479, 481-486, 488-489, 493-494, 496-497, 499-502, 505-506, 508-509, 511-512, 517-518, 521-524, 527-532, 535-553, 556-567, 569-584, 588-604, 606-610, 614-646, 648-676, 680-698, 700-706, 715, 717, 730, 734
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   53
R/estimate_proportion.R                      198      10  94.95%   421-428, 432, 437, 545
R/fit_rsp_step.R                              36       7  80.56%   103-109
R/fit_survival_step.R                         36       7  80.56%   84-90
R/footnotes.R                                  5       4  20.00%   15-16, 52-53
R/formats.R                                   88       1  98.86%   66
R/g_forest.R                                 441      42  90.48%   172, 200, 229, 252-253, 257-258, 326, 339, 343-344, 349-350, 363, 379, 426, 457, 533, 542, 614-634, 637, 648, 705, 708, 834
R/g_lineplot.R                               192     172  10.42%   164-413, 458, 466, 504-511
R/g_step.R                                    59      30  49.15%   83-120
R/g_waterfall.R                               47      47  0.00%    83-145
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    38       0  100.00%
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           74       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   248-261
R/h_stack_by_baskets.R                        65       2  96.92%   96, 143
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   254-266
R/incidence_rate.R                            93       7  92.47%   69-76
R/individual_patient_plot.R                  133     133  0.00%    71-259
R/kaplan_meier_plot.R                        532     103  80.64%   256-260, 287-290, 313-327, 371-377, 389-398, 456, 532-538, 596-598, 624-625, 627-629, 637-639, 665, 670-673, 813-815, 837-839, 845, 1030, 1253-1285
R/logistic_regression.R                      569       3  99.47%   279-280, 347
R/missing_data.R                              20       3  85.00%   29, 61, 71
R/odds_ratio.R                               106      16  84.91%   181-199
R/prop_diff_test.R                            87       0  100.00%
R/prop_diff.R                                255      65  74.51%   56-63, 190, 364, 477-546
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       164       0  100.00%
R/rtables_access.R                            21       0  100.00%
R/score_occurrences.R                         20       1  95.00%   112
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       0  100.00%
R/summarize_ancova.R                          94      14  85.11%   155-162, 171-177, 197
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_num_patients.R                    47       3  93.62%   93-95
R/summarize_patients_exposure_in_cols.R       46       0  100.00%
R/summarize_variables_in_cols.R               64      22  65.62%   35, 37, 64, 66, 90-130
R/summarize_variables.R                      212      19  91.04%   85-102, 477
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   69-77
R/survival_duration_subgroups.R              171       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       114       7  93.86%   147-153
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              95       1  98.95%   93
R/utils_grid.R                               111     111  0.00%    39-266
R/utils_rtables.R                             74       2  97.30%   317-318
R/utils.R                                    137      32  76.64%   99-149, 334
R/wrap_text.R                                 64      64  0.00%    30-105
TOTAL                                       8610    1704  80.21%

Diff against main

Filename                          Stmts    Miss  Cover
------------------------------  -------  ------  -------
R/count_occurrences_by_grade.R       +5      +2  -2.31%
TOTAL                                +5      +2  -0.01%

Results for commit: 12ddc1f

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[JiaLiu0001]

Looks good to me. Thanks @edelarua

[edelarua]

Looks good to me. Thanks @edelarua

Hey @JiaLiu0001, thanks for the review! Can you approve the PR so it can be merged? Thanks!

[JiaLiu0001]

LGTM. Thanks.