Skip to content

refactor geom sd and fix custom stat order #1393

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
Merged
merged 12 commits into from
Feb 24, 2025
Merged

refactor geom sd and fix custom stat order #1393

merged 12 commits into from
Feb 24, 2025

Conversation

Melkiades
Copy link
Contributor

Fixes #286

@Melkiades Melkiades added bug Something isn't working enhancement sme labels Feb 20, 2025
@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Feb 20, 2025 •
edited
Loading

Unit Tests Summary

    1 files     84 suites   1m 14s ⏱️
  878 tests   869 ✅   9 💤 0 ❌
1 888 runs  1 191 ✅ 697 💤 0 ❌

Results for commit 396888a.

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Feb 20, 2025 •
edited
Loading

Unit Test Performance Difference

Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
analyze_variables 👶 $+0.06$ analyze_vars_keeps_the_order_of_mixed_custom_fnc_and_defaults
analyze_variables 👶 $+0.16$ analyze_vars_warnings_for_geom_verbose_work

Results for commit 729bc37

♻️ This comment has been updated with latest results.

@github-actions GitHub Actions
Copy link
Contributor

badge

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      96       3  96.88%   235, 237-238
R/abnormal_by_marked.R                        83       8  90.36%   94-98, 274, 276-277
R/abnormal_by_worst_grade.R                   89       3  96.63%   208, 210-211
R/abnormal_lab_worsen_by_baseline.R          150      10  93.33%   194-197, 202, 204-205, 448-450
R/abnormal.R                                  73       2  97.26%   215, 217
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               153       2  98.69%   177, 272
R/count_occurrences.R                        115       1  99.13%   118
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 61       1  98.36%   123
R/count_patients_with_flags.R                 84       1  98.81%   137
R/count_values.R                              68       2  97.06%   206, 209
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      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                    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                       214       8  96.26%   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                          77       1  98.70%   189
R/summarize_colvars.R                         10       0  100.00%
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      238       8  96.64%   207-208, 401-405, 538
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                   84      12  85.71%   51-52, 64-73
R/survival_duration_subgroups.R              212       6  97.17%   124-129
R/survival_time.R                            111       0  100.00%
R/survival_timepoint.R                       124      10  91.94%   131-140
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                            124       9  92.74%   39, 46, 403-404, 526-530
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                                      11079     499  95.50%

Diff against main

Filename                                  Stmts    Miss  Cover
--------------------------------------  -------  ------  --------
R/analyze_variables.R                       +10       0  +0.06%
R/count_values.R                             +1       0  +0.04%
R/summarize_change.R                         +1       0  +0.02%
R/utils_default_stats_formats_labels.R       +5       0  +100.00%
TOTAL                                       +17       0  +0.01%

Results for commit: 7f536d3

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

edelarua
edelarua approved these changes Feb 21, 2025
View reviewed changes
Copy link
Contributor

@edelarua edelarua left a comment

Choose a reason for hiding this comment

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

Good to go!

Melkiades and others added 4 commits February 24, 2025 16:31
@Melkiades
Merge branch 'main' into 286_refactor_geom_sd_and_fix_stat_order@main
c733e44
@Melkiades @edelarua
Update R/analyze_variables.R
b48d6f8 
Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Signed-off-by: Davide Garolini <dgarolini@gmail.com>
@Melkiades
fix lintr
9277a77
@Melkiades
fix warning
396888a
@Melkiades Melkiades enabled auto-merge (squash) February 24, 2025 16:33
@Melkiades Melkiades merged commit 876b7e3 into main Feb 24, 2025
28 checks passed
@Melkiades Melkiades deleted the 286_refactor_geom_sd_and_fix_stat_order@main branch February 24, 2025 16:44
@github-actions github-actions bot locked and limited conversation to collaborators Feb 24, 2025
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Reviewers

@edelarua edelarua edelarua approved these changes

Assignees

@edelarua edelarua

Labels
bug Something isn't working enhancement sme
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Refactor geometric mean computation
2 participants
@Melkiades @edelarua