Clean up documentation #914

edelarua · 2023-05-12T14:12:27Z

Some minor documentation formatting fixes that will increase consistency across the package:

Moved export/keywords to bottom of roxygen documentation to fix spacing in examples
Increased line width in roxygen documentation in several places
Converted remaining instances of \code{} to ``
Removed unused "# nolint" instances
Removed extra blank lines and repeated @inheritParams
Removed `` from function links as they are unnecessary

These are organized in separate commits for the most part if that makes it easier to review.

Closes #913

github-actions · 2023-05-12T14:19:31Z

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%   134, 240, 258
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%   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%   74
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                     142       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    169       9  94.67%   19-20, 227-231, 275, 290, 298, 304-305
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            167      38  77.25%   232-263, 274, 371, 393-430
R/desctools_binom_diff.R                     663      66  90.05%   68, 103-104, 144-145, 148, 227, 253-262, 301, 303, 323, 327, 331, 335, 391, 394, 397, 400, 461, 469, 481-482, 488-491, 499, 502, 511, 514, 562-563, 565-566, 568-569, 571-572, 642, 654-667, 672, 719, 732, 736
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   60
R/estimate_proportion.R                      198      11  94.44%   75-82, 86, 91, 460, 565
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       3  97.39%   107, 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, 697, 700, 824
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                    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%   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           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/incidence_rate.R                            93       7  92.47%   68-75
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        569      61  89.28%   248-283, 292-296, 494, 666-668, 676-678, 703, 710-711, 881, 1065, 1312-1323
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, 258-265, 404, 464, 569
R/prune_occurrences.R                         57      10  82.46%   140-144, 190-194
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       165       4  97.58%   279, 321-323
R/rtables_access.R                            38       4  89.47%   161-164
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%   189
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, 254, 322
R/summarize_num_patients.R                    68       5  92.65%   103-105, 209-210
R/summarize_patients_exposure_in_cols.R       79       0  100.00%
R/summarize_variables.R                      217       2  99.08%   268, 485
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   64-72
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%   91
R/utils_grid.R                               111       5  95.50%   152, 262-268
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 345-346
R/utils.R                                    137      10  92.70%   105, 107, 111, 131, 134, 137, 141, 150-151, 334
TOTAL                                       8929     387  95.67%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  -------
R/kaplan_meier_plot.R       +2       0  +0.04%
TOTAL                       +2       0  +0.00%

Results for commit: e57461e

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-05-12T14:19:57Z

Unit Tests Summary

      1 files   78 suites 54s ⏱️
  729 tests 729 ✔️     0 💤 0 ❌
1 546 runs 973 ✔️ 573 💤 0 ❌

Results for commit d70db91.

♻️ This comment has been updated with latest results.

Signed-off-by: Emily de la Rua <[email protected]>

Melkiades · 2023-05-15T08:52:54Z

R/package.R

+# Resolve missing global definitions:
+utils::globalVariables(c(
+  ".",
+  "x",
+  "control_coxph",
+  "control_incidence_rate",


very interesting. This could be also a solution to the warnings in rtables? I dunno

Melkiades · 2023-05-15T09:00:55Z

R/utils.R

 #' without any warnings.
 #'
-#' @param x numeric S3 class, a sequence of numbers for which the range is computed.


what was that ahah

Melkiades

Everything looks good to me! Amazingly well done @edelarua. This will help us with debugging and understanding. Thanks :)

edelarua added 12 commits May 9, 2023 19:37

Fix examples spacing, line widths

d6e7c55

Change \code{} to ``

fa62732

Check @include instances

0378ce0

Remove unused #nolint

4f44e01

Update test snapshots

c27a37e

Remove extra newlines, remove duplicate inheritParams

34440ab

Update KM

0907e40

Merge branch 'main' into cleanup_docs@main

ac52d85

Update docs

f5c777d

Remove unnecessary backticks from function links, add missing ()s

946c4de

Remove version requirement for missing global definitions

e823612

Merge branch 'main' into 913_cleanup_docs@main

78ae741

edelarua added the sme label May 12, 2023

Update spelling

4addb53

Melkiades self-requested a review May 12, 2023 14:44

edelarua and others added 2 commits May 12, 2023 14:21

Fix .pre-commit-config.yaml

55dce4d

Signed-off-by: Emily de la Rua <[email protected]>

Fix lint

a307429

Melkiades reviewed May 15, 2023

View reviewed changes

Melkiades approved these changes May 15, 2023

View reviewed changes

shajoezhu mentioned this pull request May 15, 2023

new release tag, for OCEAN, by 2023-05-23 #917

Closed

10 tasks

edelarua added 2 commits May 15, 2023 10:14

Merge branch 'main' into 913_cleanup_docs@main

c641986

Update roxygen

d70db91

edelarua enabled auto-merge (squash) May 15, 2023 14:20

edelarua merged commit 36adf45 into main May 15, 2023

edelarua deleted the 913_cleanup_docs@main branch May 15, 2023 14:25

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Clean up documentation #914

Clean up documentation #914

edelarua commented May 12, 2023 •

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Melkiades May 15, 2023

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Clean up documentation #914

Clean up documentation #914

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Code Coverage Summary

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github-actions bot commented May 12, 2023 • edited Loading

Unit Tests Summary

Melkiades May 15, 2023

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edelarua commented May 12, 2023 •

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