Implement `na_str` argument in all columnwise analysis functions #1140

edelarua · 2023-11-24T22:18:18Z

Pull Request

Merge after insightsengineering/rtables#791

github-actions · 2023-11-24T22:24:44Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      68       2  97.06%   78-79
R/abnormal_by_marked.R                        55       5  90.91%   78-82
R/abnormal_by_worst_grade_worsen.R           116       3  97.41%   240-242
R/abnormal_by_worst_grade.R                   60       0  100.00%
R/abnormal.R                                  43       0  100.00%
R/analyze_variables.R                        190      10  94.74%   489-490, 506, 530, 686-687, 692-693, 711-712
R/analyze_vars_in_cols.R                     179      35  80.45%   168-169, 184, 207-212, 227, 241-242, 250-258, 264-270, 349-355
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        124      17  86.29%   131-135, 247, 325-334, 389-390, 396
R/control_incidence_rate.R                    20       8  60.00%   32-35, 38-41
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                          50       1  98.00%   67
R/count_missed_doses.R                        34       0  100.00%
R/count_occurrences_by_grade.R               107       4  96.26%   144-146, 149
R/count_occurrences.R                        115       1  99.13%   108
R/count_patients_events_in_cols.R             67       1  98.51%   53
R/count_patients_with_event.R                 47       0  100.00%
R/count_patients_with_flags.R                 58       4  93.10%   56-57, 62-63
R/count_values.R                              27       0  100.00%
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, 239, 254, 262, 268-269
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            173      40  76.88%   235-266, 326-328, 339, 360-397
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                  50       1  98.00%   63
R/estimate_proportion.R                      205      12  94.15%   78-85, 89, 94, 315, 482, 588
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     181       3  98.34%   145, 155, 280
R/g_forest.R                                 438      21  95.21%   199, 319, 336-337, 342-343, 356, 372, 419, 450, 526, 535, 616-620, 630, 705, 708, 832
R/g_lineplot.R                               206      34  83.50%   168, 181, 210, 236-239, 315-322, 340-341, 347-357, 449, 455, 457, 499-500, 504-505
R/g_step.R                                    68       1  98.53%   109
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                    45       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  57       2  96.49%   77-78
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           76       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        67       3  95.52%   68-69, 95
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           81       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/imputation_rule.R                           17       2  88.24%   54-55
R/incidence_rate.R                            96       7  92.71%   44-51
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        688      65  90.55%   236-239, 279-314, 323-327, 538, 725-727, 735-737, 769-770, 943-946, 1169, 1495-1506
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               109       0  100.00%
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      16  93.96%   62-65, 97, 282-289, 432, 492, 597
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             61       0  100.00%
R/response_subgroups.R                       185       4  97.84%   267, 315-317
R/riskdiff.R                                  52       7  86.54%   88-91, 100, 110-111
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       3  94.92%   73-74, 129
R/summarize_ancova.R                         101       1  99.01%   172
R/summarize_change.R                          30       0  100.00%
R/summarize_colvars.R                         13       2  84.62%   72-73
R/summarize_coxreg.R                         178       6  96.63%   201-202, 209, 346-347, 442
R/summarize_glm_count.R                      170      29  82.94%   160, 164-214, 259-260
R/summarize_num_patients.R                   103       9  91.26%   109-111, 164-165, 256-261
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   42
R/survival_biomarkers_subgroups.R             63       0  100.00%
R/survival_coxph_pairwise.R                   76       9  88.16%   51-59
R/survival_duration_subgroups.R              184       0  100.00%
R/survival_time.R                             79       0  100.00%
R/survival_timepoint.R                       113       7  93.81%   120-126
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       136       4  97.06%   72, 577-580
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             90       7  92.22%   24, 31-35, 376-377
R/utils_split_funs.R                          52       2  96.15%   81, 93
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9888     523  94.71%

Diff against main

Filename                                   Stmts    Miss  Cover
---------------------------------------  -------  ------  --------
R/analyze_vars_in_cols.R                      +1       0  +0.11%
R/h_response_biomarkers_subgroups.R           +1       0  +100.00%
R/h_survival_biomarkers_subgroups.R           +1       0  +100.00%
R/response_biomarkers_subgroups.R             +1       0  +100.00%
R/response_subgroups.R                       +15       0  +0.19%
R/summarize_colvars.R                         +1       0  +1.28%
R/summarize_coxreg.R                          +4       0  +0.08%
R/summarize_patients_exposure_in_cols.R       +1       0  +0.01%
R/survival_biomarkers_subgroups.R             +1       0  +100.00%
R/survival_duration_subgroups.R               +5       0  +100.00%
TOTAL                                        +31       0  +0.02%

Results for commit: c207924

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-11-24T22:26:55Z

Unit Tests Summary

      1 files     81 suites 1m 3s ⏱️
  804 tests   781 ✔️   23 💤 0 ❌
1 704 runs 1 056 ✔️ 648 💤 0 ❌

Results for commit c207924.

♻️ This comment has been updated with latest results.

github-actions · 2023-11-24T22:27:00Z

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	$±Time$	Test Case
response_biomarkers_subgroups	👶	$+0.74$	tabulate_rsp_biomarkers_na_str_argument_works_as_expected
response_subgroups	👶	$+0.45$	tabulate_rsp_subgroups_na_str_argument_works_as_expected
survival_biomarkers_subgroups	👶	$+0.61$	tabulate_survival_biomarkers_na_str_argument_works_as_expected
survival_duration_subgroups	👶	$+0.52$	tabulate_survival_subgroups_na_str_argument_works_as_expected

Results for commit 1e49617

♻️ This comment has been updated with latest results.

edelarua · 2023-11-24T23:00:09Z

Updated output from issue example:

                                                 B: Placebo         A: Drug X                                 
Baseline Risk Factors           Total Events   Events   Median   Events   Median   Hazard Ratio   95% Wald CI 
——————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients                        116          58      ---       58      ---         1.00       (0.69, 1.44)
Sex                                                                                                           
  F                                  68          38      ---       30      ---         0.79       (0.49, 1.28)
  M                                  48          20      ---       28      9.6         1.39       (0.78, 2.47)
Categorical Level Biomarker 2                                                                                 
  LOW                                48          21      ---       27      9.3         1.14       (0.64, 2.02)
  MEDIUM                             42          26      ---       16      ---         0.97       (0.52, 1.82)
  HIGH                               26          11      ---       15      ---         0.97       (0.45, 2.12)

tests/testthat/_snaps/survival_duration_subgroups.md

Melkiades · 2023-11-27T15:12:30Z

tests/testthat/_snaps/survival_time.md

@@ -136,13 +136,12 @@
        Median                  32.0               23.9              20.8               24.9      
          95% CI            (22.6, 53.4)       (18.3, 32.9)      (12.9, 26.0)       (21.5, 31.7)  
        25% and 75%-ile      17.4, 65.3         9.8, 42.7          7.3, 37.1         11.5, 49.3   
-        Range             0.3 to 155.5 {1}   0.1 to 154.1 {2}   0.6 to 80.7 {3}   0.1 to 155.5 {4}
+        Range             0.3 to 155.5 {1}   0.1 to 154.1 {2}   0.6 to 80.7 {3}   0.1 to 155.5 {1}


why did this escape :D

Melkiades

Lgtm!! :)) Thanks Emily for this swift fix of na_str in colvars. I think if there are still some functions w/o we can still add it at a later time

edelarua added 6 commits November 24, 2023 13:46

Add na_str argument to all analyze_colvars, tabulation functions

eceee3d

Update unrelated snapshot

4773446

Update NEWS

84d364a

Update docs

bb333a6

Add na_str to tabulate_rsp_groups, tabulate_survival_subgroups

5a86393

Add tests for na_str in tabulation functions

d413be1

edelarua added the sme label Nov 24, 2023

Fix

c207924

Melkiades reviewed Nov 27, 2023

View reviewed changes

tests/testthat/_snaps/survival_duration_subgroups.md Show resolved Hide resolved

Melkiades reviewed Nov 27, 2023

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Melkiades approved these changes Nov 27, 2023

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shajoezhu mentioned this pull request Nov 27, 2023

[CRAN Release]: <v0.9.3> #1084

Closed

32 tasks

edelarua merged commit 2bfd695 into main Nov 27, 2023
24 checks passed

edelarua deleted the 790_analyze_colvars_na_str@main branch November 27, 2023 19:51

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Implement `na_str` argument in all columnwise analysis functions #1140

Implement `na_str` argument in all columnwise analysis functions #1140

edelarua commented Nov 24, 2023

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edelarua commented Nov 24, 2023

Melkiades Nov 27, 2023

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Implement na_str argument in all columnwise analysis functions #1140

Implement na_str argument in all columnwise analysis functions #1140

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edelarua commented Nov 24, 2023

Pull Request

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Code Coverage Summary

Diff against main

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Unit Tests Summary

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Unit Test Performance Difference

edelarua commented Nov 24, 2023

Melkiades Nov 27, 2023

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Implement `na_str` argument in all columnwise analysis functions #1140

Implement `na_str` argument in all columnwise analysis functions #1140

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