Add Value documentation for all functions

[edelarua]

Closes #871

Also updated "Functions" section or "Notes" section for clarity where necessary. Applied the same structure for all statistics/formatted analysis/analyze function documentation.

E.g. count_occurrences:

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   124-128
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_vars_in_cols.R                      37       1  97.30%   113
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        138       3  97.83%   132, 235, 254
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                          47       1  97.87%   60
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%   73
R/count_patients_with_event.R                 72       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    168       7  95.83%   227-231, 276, 291, 299, 305-306
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            167      38  77.25%   237-268, 279, 377, 399-436
R/desctools_binom_diff.R                     663      66  90.05%   68, 103-104, 144-145, 148, 227, 253-262, 301, 303, 323, 327, 331, 335, 390, 393, 396, 399, 460, 468, 480-481, 487-490, 498, 501, 510, 513, 561-562, 564-565, 567-568, 570-571, 641, 653-666, 671, 718, 731, 735
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   58
R/estimate_proportion.R                      198      11  94.44%   75-82, 86, 91, 462, 567
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formats.R                                  115       3  97.39%   104, 142, 152
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, 697, 700, 824
R/g_lineplot.R                               199      29  85.43%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 445, 453
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        74       0  100.00%
R/h_biomarkers_subgroups.R                    38       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           74       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   258-271
R/h_stack_by_baskets.R                        65       1  98.46%   96
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   260-272
R/incidence_rate.R                            93       7  92.47%   68-75
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        567      61  89.24%   258-293, 302-306, 503, 676-678, 686-688, 714, 721-722, 899, 1084, 1334-1345
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                                255      12  95.29%   98, 259-266, 408, 470, 579
R/prune_occurrences.R                         57      10  82.46%   141-145, 191-195
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       165       4  97.58%   278, 320-322
R/rtables_access.R                            38       4  89.47%   163-166
R/score_occurrences.R                         20       1  95.00%   123
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   78-79, 136
R/summarize_ancova.R                          95       1  98.95%   192
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_coxreg.R                         140       0  100.00%
R/summarize_glm_count.R                      164       4  97.56%   188, 193, 258, 327
R/summarize_num_patients.R                    68       5  92.65%   98-100, 204-205
R/summarize_patients_exposure_in_cols.R       47       0  100.00%
R/summarize_variables.R                      217       2  99.08%   275, 493
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   65-73
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       114       7  93.86%   150-156
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              87       1  98.85%   92
R/utils_grid.R                               111       5  95.50%   153, 265-271
R/utils_rtables.R                             86       7  91.86%   25, 32-36, 350-351
R/utils.R                                    137      10  92.70%   101, 103, 107, 129, 132, 135, 139, 148-149, 337
TOTAL                                       8894     385  95.67%

Diff against main

Filename             Stmts    Miss  Cover
-----------------  -------  ------  -------
R/decorate_grob.R        0     +32  -19.16%
TOTAL                    0     +32  -0.36%

Results for commit: c606405

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

       1 files    77 suites   1m 0s ⏱️
   726 tests 726 ✔️     0 💤 0 ❌
1 541 runs  971 ✔️ 570 💤 0 ❌

Results for commit ef246f0.

♻️ This comment has been updated with latest results.

[Melkiades]

Really Amazing work!! Thanks so much! This makes things MUCH clearer to understand and the underlying components are more evident now. This PR is probably fixing a couple more issues about structure that I filed months ago. We should check if also those are completed by this!

Just see the comments and fix what you think is appropriate, then you can merge ;)