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 a_count_occurrences_by_grade() #1332

Merged
merged 1 commit into from
Oct 22, 2024
Merged

Refactor a_count_occurrences_by_grade() #1332

merged 1 commit into from
Oct 22, 2024

Conversation

edelarua
Copy link
Contributor

Pull Request

Fixes #1331

@edelarua edelarua added the sme label Oct 18, 2024
@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 18, 2024 •
edited
Loading

Unit Tests Summary

    1 files     84 suites   1m 12s ⏱️
  860 tests   849 ✅  11 💤 0 ❌
1 847 runs  1 161 ✅ 686 💤 0 ❌

Results for commit 9da3fff.

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 18, 2024 •
edited
Loading

Unit Test Performance Difference

Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
count_occurrences_by_grade 👶 $+0.02$ a_count_occurrences_by_grade_works_with_custom_input.
count_occurrences_by_grade 👶 $+0.02$ a_count_occurrences_by_grade_works_with_healthy_input.
count_occurrences_by_grade 👶 $+0.20$ summarize_occurrences_works_as_expected_with_risk_difference_column

Results for commit 44416cb

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Oct 18, 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%   92-96
R/abnormal_by_worst_grade_worsen.R           116       3  97.41%   262-264
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%   492, 632
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%   255, 314
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                          50       1  98.00%   73
R/count_missed_doses.R                        34       0  100.00%
R/count_occurrences_by_grade.R               157       2  98.73%   176, 270
R/count_occurrences.R                        115       1  99.13%   115
R/count_patients_events_in_cols.R             67       1  98.51%   59
R/count_patients_with_event.R                 47       0  100.00%
R/count_patients_with_flags.R                 58       0  100.00%
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%   64
R/estimate_proportion.R                      205      11  94.63%   82-89, 93, 98, 319, 485
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%   66-71, 151
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%   69-72, 104, 289-296, 439, 604
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%   182, 187
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%   192-193, 489
R/summarize_num_patients.R                    93       4  95.70%   116-118, 265
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   55
R/survival_biomarkers_subgroups.R             78       6  92.31%   117-122
R/survival_coxph_pairwise.R                   79      11  86.08%   50-51, 63-71
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%   124-130
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                                      10566     460  95.65%

Diff against main

Filename                          Stmts    Miss  Cover
------------------------------  -------  ------  -------
R/count_occurrences_by_grade.R      +44      +1  -0.39%
TOTAL                               +44      +1  +0.01%

Results for commit: 9da3fff

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

@shajoezhu shajoezhu changed the base branch from main to 1325_occurrences_by_grade_denom@main October 22, 2024 02:30
@shajoezhu shajoezhu force-pushed the 1331_refactor_count_occ_grd@main branch from 9da3fff to 9978938 Compare October 22, 2024 05:47
@shajoezhu shajoezhu force-pushed the 1325_occurrences_by_grade_denom@main branch from 00d113a to 40335d8 Compare October 22, 2024 05:55
@shajoezhu shajoezhu force-pushed the 1331_refactor_count_occ_grd@main branch from 9978938 to 715f42d Compare October 22, 2024 06:16
@shajoezhu shajoezhu force-pushed the 1325_occurrences_by_grade_denom@main branch from 40335d8 to 22936ca Compare October 22, 2024 06:19
@shajoezhu shajoezhu force-pushed the 1331_refactor_count_occ_grd@main branch from 715f42d to 17047d3 Compare October 22, 2024 06:48
@shajoezhu shajoezhu merged commit 30ebc5b into 1325_occurrences_by_grade_denom@main Oct 22, 2024
1 check passed
@shajoezhu shajoezhu deleted the 1331_refactor_count_occ_grd@main branch October 22, 2024 06:51
@github-actions github-actions bot locked and limited conversation to collaborators Oct 22, 2024
Melkiades
Melkiades reviewed Oct 22, 2024
View reviewed changes
NEWS.md
@@ -3,6 +3,7 @@
### Enhancements
* Added the `denom` parameter to `s_count_cumulative()`, `s_count_missed_doses()`, and `s_count_occurrences_by_grade()`.
* Added `"N_row"` as an optional input to `denom` in `s_count_occurrences()`.
* Refactored `a_count_occurrences_by_grade()` to no longer use `make_afun()`.
Copy link
Contributor

Choose a reason for hiding this comment

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

This is very nice. Thanks Emily for bringing this forward

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Reviewers

@Melkiades Melkiades Melkiades left review comments

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

Successfully merging this pull request may close these issues.

Refactor a_count_occurrences_by_grade()
3 participants
@edelarua @Melkiades @shajoezhu