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reduce the amount of spelling issues / WORDLIST #971

Merged
merged 7 commits into from
Jun 20, 2023
Merged

reduce the amount of spelling issues / WORDLIST #971

merged 7 commits into from
Jun 20, 2023

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m7pr
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@m7pr m7pr commented Jun 16, 2023

The follow-up after https://github.com/insightsengineering/coredev-tasks/issues/235

Final spelling::spell_check_package() output. Some or inherited by car::Anova parameters and most of them are surnames which I left

  WORD            FOUND IN
Anova           try_car_anova.Rd:31
biomarker       control_step.Rd:16,21,26,32,33,34,41
                extract_rsp_biomarkers.Rd:42
                extract_survival_biomarkers.Rd:39
                fit_rsp_step.Rd:20
                fit_survival_step.Rd:23
                g_step.Rd:19,35
                h_response_biomarkers_subgroups.Rd:19,26,74,78
                h_step.Rd:40,72,82,97
                h_survival_biomarkers_subgroups.Rd:19,25,76,79
                h_tab_one_biomarker.Rd:10
                response_biomarkers_subgroups.Rd:33,38
                survival_biomarkers_subgroups.Rd:36,41,51
                NEWS.md:322
Biomarker       h_response_biomarkers_subgroups.Rd:8
                h_survival_biomarkers_subgroups.Rd:8
                h_tab_one_biomarker.Rd:5
                response_biomarkers_subgroups.Rd:6
                survival_biomarkers_subgroups.Rd:6
biomarkers      extract_rsp_biomarkers.Rd:39
                extract_survival_biomarkers.Rd:37
                h_response_biomarkers_subgroups.Rd:51,72
                h_survival_biomarkers_subgroups.Rd:53,73
Biomarkers      extract_rsp_biomarkers.Rd:5
                extract_survival_biomarkers.Rd:5
Bové           tern-package.Rd:24
Clopper         h_proportions.Rd:64
coercible       h_cox_regression.Rd:41,45
Forkers         README.md:75,85
funder          tern-package.Rd:36
Haenszel        h_prop_diff_test.Rd:35
Hauck           h_prop_diff.Rd:59
Hoffmann        tern-package.Rd:36
Jeffreys        h_proportions.Rd:73,74
Kaplan          g_km.Rd:5,109,111,114,116
                h_ggkm.Rd:61,63,71
                h_km_layout.Rd:19,27
                NEWS.md:560
                README.md:30
                tern.Rmd:60
Kenward         try_car_anova.Rd:18
layouting       abnormal.Rd:78
                abnormal_by_baseline.Rd:78
                abnormal_by_marked.Rd:74
                abnormal_by_worst_grade.Rd:69
                abnormal_by_worst_grade_worsen.Rd:75
                analyze_vars_in_cols.Rd:59
                compare_variables.Rd:128
                count_cumulative.Rd:85
                count_missed_doses.Rd:73
                count_occurrences.Rd:101
                count_occurrences_by_grade.Rd:104,110
                count_patients_events_in_cols.Rd:71
                count_patients_with_event.Rd:89
                count_patients_with_flags.Rd:91
                count_values_funs.Rd:96
                cox_regression.Rd:120,147
                estimate_multinomial_rsp.Rd:63
                estimate_proportions.Rd:105
                incidence_rate.Rd:99
                logistic_regression_cols.Rd:15
                odds_ratio.Rd:94
                prop_diff.Rd:98
                prop_diff_test.Rd:91
                split_cols_by_groups.Rd:24
                summarize_ancova.Rd:111
                summarize_change.Rd:62
                summarize_colvars.Rd:32
                summarize_glm_count.Rd:106
                summarize_logistic.Rd:25
                summarize_num_patients.Rd:110,116
                summarize_patients_exposure_in_cols.Rd:108,115
                summarize_variables.Rd:243
                survival_coxph_pairwise.Rd:106
                survival_time.Rd:83
                survival_timepoint.Rd:146
poisson         h_glm_count.Rd:42,71,76
pre             abnormal_by_baseline.Rd:46
                abnormal_by_worst_grade.Rd:79,89
                compare_variables.Rd:177,181
                cox_regression.Rd:104
                h_ggkm.Rd:27
                h_grob_tbl_at_risk.Rd:10
                h_km_layout.Rd:10
                h_xticks.Rd:10
                s_cox_multivariate.Rd:38
                summarize_variables.Rd:294,301
                NEWS.md:405
                tern.Rmd:54,87
                tern_formats.Rmd:198,278
quasipoisson    h_glm_count.Rd:42,73,76
repo            NEWS.md:84
                README.md:9,15,83,85
responder       argument_convention.Rd:76
                check_diff_prop_ci.Rd:10,24
                estimate_proportions.Rd:48
                h_prop_diff.Rd:30
                h_proportions.Rd:33
                h_response_subgroups.Rd:32
                prop_diff.Rd:109
                NEWS.md:436,438,439
                tables.Rmd:358
responders      estimate_proportions.Rd:113
                odds_ratio.Rd:126
                response_subgroups.Rd:28,29
                NEWS.md:201
                tables.Rmd:352,353,367
Sabanés        tern-package.Rd:24
Satterthwaite   try_car_anova.Rd:19
Schouten        h_prop_diff_test.Rd:38,93
                NEWS.md:456,464
                tables.Rmd:427
subtable        score_occurrences.Rd:36,60
subtables       response_biomarkers_subgroups.Rd:48
                score_occurrences.Rd:48,60
                survival_biomarkers_subgroups.Rd:57
TLG             description:1
                NEWS.md:596
                README.md:68
TLGs            title:1
                NEWS.md:533,584
unformatted     cox_regression.Rd:275
unstratified    h_tbl_coxph_pairwise.Rd:37
                odds_ratio.Rd:106
                prop_diff.Rd:118
                s_cox_multivariate.Rd:37
                survival_coxph_pairwise.Rd:114
                NEWS.md:30

@m7pr m7pr self-assigned this Jun 16, 2023
@m7pr m7pr added documentation Improvements or additions to documentation core labels Jun 16, 2023
@m7pr m7pr requested review from edelarua and Melkiades June 16, 2023 14:09
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m7pr commented Jun 16, 2023

cc @edelarua @Melkiades

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github-actions bot commented Jun 16, 2023 •
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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_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                    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%   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                     142       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    169       9  94.67%   19-20, 213-217, 261, 276, 284, 290-291
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                      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, 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/summarize_variables.R                      220       2  99.09%   266, 492
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                                       9124     424  95.35%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 250fcf8

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Jun 16, 2023 •
edited
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Unit Tests Summary

       1 files    78 suites   59s ⏱️
   735 tests 735 ✔️     0 💤 0 ❌
1 560 runs  979 ✔️ 581 💤 0 ❌

Results for commit 458035d.

♻️ This comment has been updated with latest results.

@shajoezhu shajoezhu marked this pull request as draft June 16, 2023 14:25
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Thanks @m7pr , i m blocking this after the release

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m7pr commented Jun 19, 2023

@shajoezhu maybe you can take the benefit of this change, before the release? It mostly fixes spelling issues and cleans up the documenation

Melkiades
Melkiades reviewed Jun 19, 2023
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Melkiades
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Melkiades
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In general, it seems all fine. For me, it is ok to merge it in before release too. Thank you for polishing the WORDLIST

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hi @Melkiades and @m7pr , many thanks for looking into this PR. Usually, I would agree for fixing these items. However, we were in the middle of submitting to cran, and this PR came was large amont of files were touched. I was inclined to have someone have a proper review before merging in. anyway, let's see the the most recent feedback from cran, if CRAN still requies more changes, I will do the submission after this PR is merged in. hi @edelarua and @ayogasekaram , would you guys have another look at this please

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m7pr commented Jun 19, 2023

@shajoezhu I was not aware that today it was a big CRAN submission! Great job on the release!

edelarua
edelarua approved these changes Jun 19, 2023
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Lgtm! The tern submission to CRAN is done so this should be fine to go in now.

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Lgtm! The tern submission to CRAN is done so this should be fine to go in now.

Yes, definitely! Thanks a lot guys!

@Melkiades Melkiades marked this pull request as ready for review June 20, 2023 07:42
Melkiades and others added 5 commits June 20, 2023 09:42
@Melkiades
Merge branch 'main' into update_wordlist@main
9c58678 
Signed-off-by: Davide Garolini <davide.garolini@roche.com>
@m7pr
fix passive aggresive voice for spellcheck
565019d
@m7pr
merge
be583c7 
Merge branch 'update_wordlist@main' of https://github.com/insightsengineering/tern into update_wordlist@main

# Conflicts:
#	NEWS.md
@m7pr
escape one more parameter
aed901b
@m7pr
fix GHA checks
458035d
@m7pr m7pr mentioned this pull request Jun 20, 2023
Merged
@m7pr m7pr merged commit 15bd988 into main Jun 20, 2023
@m7pr m7pr deleted the update_wordlist@main branch June 20, 2023 10:00
@shajoezhu shajoezhu mentioned this pull request Jun 20, 2023
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