`summarize_vars` renamed into `analyze_vars` and aliases + deprecation cycle #982

Melkiades · 2023-06-21T13:35:57Z

Fixes #900

github-actions · 2023-06-21T13:43:34Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      62       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   115-119
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   233-235
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_variables.R                        220       2  99.09%   273, 499
R/analyze_vars_in_cols.R                     113      23  79.65%   164, 188-193, 206, 219-225, 268-274, 305
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        139       5  96.40%   126-127, 137, 241, 259
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                          47       1  97.87%   63
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       6  92.86%   156-158, 161, 176-177
R/count_occurrences.R                         61       1  98.36%   92
R/count_patients_events_in_cols.R             67       1  98.51%   62
R/count_patients_with_event.R                 33       0  100.00%
R/count_patients_with_flags.R                 39       0  100.00%
R/count_values.R                              24       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                            169      40  76.33%   232-263, 323-325, 332, 353-390
R/desctools_binom_diff.R                     663      66  90.05%   55, 90-91, 131-132, 135, 214, 240-249, 288, 290, 310, 314, 318, 322, 378, 381, 384, 387, 448, 456, 468-469, 475-478, 486, 489, 498, 501, 549-550, 552-553, 555-556, 558-559, 629, 641-654, 659, 706, 719, 723
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   60
R/estimate_proportion.R                      199      12  93.97%   75-82, 86, 91, 294, 461, 566
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       2  98.26%   145, 155
R/g_forest.R                                 437      23  94.74%   197, 248-249, 316, 333-334, 339-340, 353, 369, 416, 447, 523, 532, 613-617, 627, 702, 705, 829
R/g_lineplot.R                               199      29  85.43%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 449
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        74       0  100.00%
R/h_biomarkers_subgroups.R                    40       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                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        65       1  98.46%   91
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/incidence_rate.R                            93       7  92.47%   55-62
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        630      61  90.32%   260-295, 304-308, 508, 680-682, 690-692, 717, 724-725, 897, 1086, 1403-1414
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            88       0  100.00%
R/prop_diff.R                                260      16  93.85%   72-75, 107, 267-274, 413, 473, 578
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   273, 315-317
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                                      47       3  93.62%   73-74, 129
R/summarize_ancova.R                          95       1  98.95%   180
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_coxreg.R                         156       2  98.72%   198, 410
R/summarize_glm_count.R                      164       4  97.56%   159, 164, 208, 261
R/summarize_num_patients.R                    74       9  87.84%   103-105, 150-151, 217-222
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   56
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   59-67
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       116       7  93.97%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              87       1  98.85%   84
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 346-347
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9145     430  95.30%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  --------
R/analyze_variables.R     +220      +2  +99.09%
TOTAL                     +220      +2  +100.00%

Results for commit: 055cffe

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-06-21T14:03:27Z

Unit Tests Summary

      1 files   78 suites 58s ⏱️
  739 tests 739 ✔️     0 💤 0 ❌
1 568 runs 985 ✔️ 583 💤 0 ❌

Results for commit eee4ef4.

♻️ This comment has been updated with latest results.

NEWS.md

Signed-off-by: Davide Garolini <dgarolini@gmail.com>

shajoezhu · 2023-06-22T00:58:16Z

let's investigate downstream break changes in the NEST pipeline. and use staged.dependencies to update before merging this in.

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

R/analyze_variables.R

shajoezhu

lgtm! Thanks a lot @Melkiades

BFalquet

Looks fine tom me, thank you for the work, would you like to already set up the deprecation warning?

Melkiades added 4 commits June 21, 2023 15:12

renaming + aliases

216b21d

init modification of tests and examples

6584a50

do not forget the docs!

7c836b2

renaming test updates

c62e498

Melkiades added enhancement sme labels Jun 21, 2023

Melkiades and others added 2 commits June 21, 2023 13:35

Merge c62e498 into 605de00

fcf5305

[skip actions] Restyle files

8d96cff

Melkiades added 2 commits June 21, 2023 15:45

empty

9afe494

fixing main

cb93767

Melkiades commented Jun 21, 2023

View reviewed changes

NEWS.md Outdated Show resolved Hide resolved

Update NEWS.md

ad0d707

Signed-off-by: Davide Garolini <dgarolini@gmail.com>

Merge branch 'main' into 900_aliases_analyze@main

4d9d7f0

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

Melkiades commented Jun 22, 2023

View reviewed changes

R/analyze_variables.R Show resolved Hide resolved

shajoezhu mentioned this pull request Jun 24, 2023

prep for v0.8.4 #978

Closed

4 tasks

Melkiades added 2 commits June 26, 2023 10:34

Merge branch 'main' into 900_aliases_analyze@main

cacda04

Merge branch 'main' into 900_aliases_analyze@main

d3f7a7b

shajoezhu mentioned this pull request Jun 27, 2023

prep for release v0.9.0 #990

Closed

18 tasks

Merge branch 'main' into 900_aliases_analyze@main

eee4ef4

shajoezhu approved these changes Jul 4, 2023

View reviewed changes

Melkiades merged commit ee89e1e into main Jul 4, 2023

Melkiades deleted the 900_aliases_analyze@main branch July 4, 2023 07:59

BFalquet reviewed Jul 4, 2023

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Melkiades mentioned this pull request Jul 14, 2023

Enhance deprecation messages for summarize_* to analyze_* shifts #1006

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`summarize_vars` renamed into `analyze_vars` and aliases + deprecation cycle #982

`summarize_vars` renamed into `analyze_vars` and aliases + deprecation cycle #982

Melkiades commented Jun 21, 2023

github-actions bot commented Jun 21, 2023 •

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shajoezhu commented Jun 22, 2023 •

edited by Melkiades

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summarize_vars renamed into analyze_vars and aliases + deprecation cycle #982

summarize_vars renamed into analyze_vars and aliases + deprecation cycle #982

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Melkiades commented Jun 21, 2023

github-actions bot commented Jun 21, 2023 • edited Loading

Code Coverage Summary

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Unit Tests Summary

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`summarize_vars` renamed into `analyze_vars` and aliases + deprecation cycle #982

`summarize_vars` renamed into `analyze_vars` and aliases + deprecation cycle #982

github-actions bot commented Jun 21, 2023 •

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github-actions bot commented Jun 21, 2023 •

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shajoezhu commented Jun 22, 2023 •

edited by Melkiades

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