1425 feature request export various internal functions for usage in jj based sister package to nest tern

[iaugusty]

Pull Request

addresses #1425, export several internal functions

[github-actions]

Unit Tests Summary

    1 files     85 suites   1m 21s ⏱️
  886 tests   877 ✅   9 💤 0 ❌
1 905 runs  1 205 ✅ 700 💤 0 ❌

Results for commit b52ff79.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
prop_diff	👶		$+0.01$	check_diff_prop_ci_fails_with_wrong_input
prop_diff	👶		$+0.01$	check_diff_prop_ci_is_silent_with_healthy_input
utils	👶		$+0.01$	clogit_with_tryCatch_fails_with_wrong_input
utils	👶		$+0.05$	clogit_with_tryCatch_is_silent_with_healthy_input
utils	👶		$+0.11$	clogit_with_tryCatch_works_with_healthy_input

Results for commit 2a07d27

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                     101       3  97.03%   242, 244-245
R/abnormal_by_marked.R                        88       8  90.91%   94-98, 281, 283-284
R/abnormal_by_worst_grade.R                   94       3  96.81%   215, 217-218
R/abnormal_lab_worsen_by_baseline.R          159      10  93.71%   205-208, 213, 215-216, 459-461
R/abnormal.R                                  78       2  97.44%   222, 224
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                         115       4  96.52%   74, 270-271, 273
R/count_missed_doses.R                        89       4  95.51%   206-209
R/count_occurrences_by_grade.R               169       8  95.27%   178, 386, 388, 465, 467, 469, 473-474
R/count_occurrences.R                        137      10  92.70%   119, 262-264, 330-332, 334, 338-339
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 73       2  97.26%   220, 223
R/count_patients_with_flags.R                 93       2  97.85%   234, 236
R/count_values.R                              61       2  96.72%   193, 196
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                  86       4  95.35%   65, 212, 214-215
R/estimate_proportion.R                      240       7  97.08%   88, 99, 255, 257-258, 389, 553
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%   222, 396-403, 442-452, 561, 569
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                    91      23  74.73%   40-42, 84-103
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           77      12  84.42%   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           73       6  91.78%   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                           103       7  93.20%   68-73, 242
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               157       4  97.45%   270-273
R/prop_diff_test.R                           144       2  98.61%   250, 252
R/prop_diff.R                                318      17  94.65%   71-74, 106, 299, 301, 387-394, 537, 702
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R            124      10  91.94%   88-91, 270-275
R/response_subgroups.R                       251      16  93.63%   100-105, 271-275, 280, 282-283, 310-311
R/riskdiff.R                                  65       4  93.85%   94-97
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                         150       2  98.67%   327-328
R/summarize_change.R                          72       3  95.83%   175, 177-178
R/summarize_colvars.R                         13       1  92.31%   75
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      269      10  96.28%   129-130, 202-203, 459-463, 596
R/summarize_num_patients.R                   121      10  91.74%   122-124, 244, 248, 252-253, 337-338, 340
R/summarize_patients_exposure_in_cols.R      155       7  95.48%   58, 232-233, 237, 357-358, 362
R/survival_biomarkers_subgroups.R            136      10  92.65%   117-122, 228-231
R/survival_coxph_pairwise.R                  124       5  95.97%   52-53, 248, 250-251
R/survival_duration_subgroups.R              249      15  93.98%   124-129, 268-273, 286, 288-289
R/survival_time.R                            120       1  99.17%   251
R/survival_timepoint.R                       153       2  98.69%   320, 322
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       196       0  100.00%
R/utils_factor.R                              87       1  98.85%   99
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            125       9  92.80%   39, 46, 414-415, 537-541
R/utils_split_funs.R                          52       2  96.15%   82, 94
R/utils.R                                    143       7  95.10%   131, 134, 137, 141, 150-151, 345
TOTAL                                      11966     580  95.15%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  -------
R/utils.R        +2       0  +0.07%
TOTAL            +2       0  +0.00%

Results for commit: b52ff79

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[shajoezhu]

hi @iaugusty , can you please update the news, and fix the style and add entries to pkgdown.yml file

[iaugusty]

hi @shajoezhu, in NEWS.md, should I mention which functions are now exported, or would an overall sentence like

• Exported various functions that were internal in prior release.
  under the Enhancements paragraph
  be sufficient?

Or would you prefer that I add this to ### Miscellaneous, like was done for
Converted as_factor_keep_attributes() to an exported function.
And that I add a line per exported function.

[Melkiades]

hi @shajoezhu, in NEWS.md, should I mention which functions are now exported, or would an overall sentence like

• Exported various functions that were internal in prior release.
  under the Enhancements paragraph
  be sufficient?

Or would you prefer that I add this to ### Miscellaneous, like was done for Converted as_factor_keep_attributes() to an exported function. And that I add a line per exported function.

I would add the specific names into miscellaneous as it was done for as_factor_keep_attributes()

[Melkiades]

For me, it is already good to go. Thanks!! Just fyi, the lintr error appears only now because lintr processing analyzes only changed files. It is only one line that has a return() that is not needed ;)

[Melkiades]

Lgtm! Thanks