Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Refactor count_patients_with_event() and count_patients_with_flags() #1343

Merged
merged 6 commits into from
Nov 2, 2024
Merged

Refactor count_patients_with_event() and count_patients_with_flags() #1343

merged 6 commits into from
Nov 2, 2024

Conversation

edelarua
Copy link
Contributor

Pull Request

Fixes #1342

@edelarua edelarua added the sme label Oct 25, 2024
@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 25, 2024 •
edited
Loading

Unit Tests Summary

    1 files     84 suites   1m 11s ⏱️
  868 tests   857 ✅  11 💤 0 ❌
1 863 runs  1 169 ✅ 694 💤 0 ❌

Results for commit 515818b.

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 25, 2024 •
edited
Loading

Unit Test Performance Difference

Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
count_patients_with_event 👶 $+0.02$ a_count_patients_with_event_works_with_custom_input.
count_patients_with_event 👶 $+0.02$ a_count_patients_with_event_works_with_healthy_input.
count_patients_with_flags 👶 $+0.02$ a_count_patients_with_flags_works_with_custom_input.
count_patients_with_flags 👶 $+0.03$ a_count_patients_with_flags_works_with_healthy_input.

Results for commit ca124b7

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 25, 2024 •
edited
Loading

badge

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      65       0  100.00%
R/abnormal_by_marked.R                        55       5  90.91%   93-97
R/abnormal_by_worst_grade_worsen.R           116       3  97.41%   263-265
R/abnormal_by_worst_grade.R                   60       0  100.00%
R/abnormal.R                                  43       0  100.00%
R/analyze_variables.R                        166       2  98.80%   486, 626
R/analyze_vars_in_cols.R                     176      13  92.61%   178, 221, 235-236, 244-252
R/bland_altman.R                              92       1  98.91%   46
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                         84       2  97.62%   257, 316
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               157       2  98.73%   177, 271
R/count_occurrences.R                        116       1  99.14%   120
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 62       1  98.39%   123
R/count_patients_with_flags.R                 94       1  98.94%   134
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, 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                  50       1  98.00%   65
R/estimate_proportion.R                      205      11  94.63%   83-90, 94, 99, 320, 486
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      59  89.91%   241, 253-256, 261-262, 278, 288-291, 336-339, 346, 415, 502, 515, 519-520, 525-526, 539, 555, 602, 633, 708, 717, 723, 742, 797-817, 820, 831, 850, 905, 908, 1043-1048
R/g_ipp.R                                    133       0  100.00%
R/g_km.R                                     350      57  83.71%   286-289, 308-310, 364-367, 401, 429, 433-476, 483-487
R/g_lineplot.R                               243      22  90.95%   196, 370-377, 416-426, 518, 526
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                    46       0  100.00%
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           90      12  86.67%   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           88       6  93.18%   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                            86       7  91.86%   67-72, 152
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               117       0  100.00%
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             69       6  91.30%   196-201
R/response_subgroups.R                       213       8  96.24%   100-105, 260-261
R/riskdiff.R                                  65       5  92.31%   102-105, 114
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                         106       2  98.11%   183, 188
R/summarize_change.R                          30       0  100.00%
R/summarize_colvars.R                         10       0  100.00%
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      209       3  98.56%   193-194, 490
R/summarize_num_patients.R                    93       4  95.70%   117-119, 266
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   56
R/survival_biomarkers_subgroups.R             78       6  92.31%   117-122
R/survival_coxph_pairwise.R                   79      11  86.08%   51-52, 64-72
R/survival_duration_subgroups.R              211       6  97.16%   124-129
R/survival_time.R                             79       0  100.00%
R/survival_timepoint.R                       113       7  93.81%   125-131
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       124       0  100.00%
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            100       4  96.00%   39, 46, 403-404
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                                      10629     462  95.65%

Diff against main

Filename                         Stmts    Miss  Cover
-----------------------------  -------  ------  -------
R/count_patients_with_event.R      +15      +1  -1.61%
R/count_patients_with_flags.R      +36      +1  -1.06%
TOTAL                              +51      +2  +0.00%

Results for commit: ee313cf

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

Melkiades
Melkiades approved these changes Oct 29, 2024
View reviewed changes
Copy link
Contributor

@Melkiades Melkiades left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Lgtm! Thanks Emily!!! I am so happy to see understandable code again. Great job!

@shajoezhu shajoezhu enabled auto-merge (squash) November 2, 2024 09:47
@shajoezhu shajoezhu merged commit d6c0ee9 into main Nov 2, 2024
28 checks passed
@shajoezhu shajoezhu deleted the 1342_afun_count_pts@main branch November 2, 2024 09:49
@github-actions github-actions bot locked and limited conversation to collaborators Nov 2, 2024
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Reviewers

@Melkiades Melkiades Melkiades approved these changes

Assignees
No one assigned
Labels
sme
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Refactor count_patients_with_event() and count_patients_with_flags()
3 participants
@edelarua @Melkiades @shajoezhu