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reduce the amount of spelling issues / WORDLIST #685

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merged 9 commits into from
Jul 28, 2023
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@m7pr m7pr commented Jul 12, 2023

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

I am basically trying to catch all spelling issues, and try to put \code{} around parameter names, function names, package names, object names and data structure names.

inst/WORDLIST was reduced from 233 words to 71 words

Final result of spelling::spell_check_package()

  WORD               FOUND IN
amongst            formatters_methods.Rd:186
                   gen_args.Rd:68
                   insert_row_at_path.Rd:20
                   int_methods.Rd:1192
                   label_at_path.Rd:17
                   make_afun.Rd:60
                   sort_at_path.Rd:21
                   ttap.Rd:17
Arg                compat_args.Rd:5,34
                   constr_args.Rd:5,124
                   lyt_args.Rd:5,208
                   sf_args.Rd:5,23
Carreras           README.md:199
                   README.Rmd:146
charset            build_table.Rd:41
                   gen_args.Rd:92
                   rtable.Rd:27
                   tabclasses.Rd:108
                   NEWS.md:113
Chohan             README.md:199
                   README.Rmd:146
combinatorial      split_functions.Rmd:147
CRAN's             NEWS.md:182
customizations     split_functions.Rmd:257
decrementing       paginate.Rd:172
dimensioned        head_tail.Rd:41
dplyr              tabulation_dplyr.Rmd:2
emph               custom_appearance.Rmd:108,248
facetted           qtable.Rd:58
facetting          qtable.Rd:27,29,51
formatter          CellValue.Rd:20
                   compat_args.Rd:18
                   format_rcell.Rd:21
                   rcell.Rd:35
                   rheader.Rd:15
                   rrow.Rd:16
                   rrowl.Rd:16
                   rtable.Rd:20
getter             col_accessors.Rd:123
                   NEWS.md:105
getters            formatters_methods.Rd:200
Godwin             README.md:199
                   README.Rmd:146
Heng               README.md:199
                   README.Rmd:146
ing                NEWS.md:92,107
initializer        custom_appearance.Rmd:116,170,176
Kelkhoff           NEWS.md:327
layouting          add_colcounts.Rd:18
                   add_existing_table.Rd:22
                   add_overall_col.Rd:17
                   analyze.Rd:73
                   analyze_colvars.Rd:49
                   append_topleft.Rd:16
                   basic_table.Rd:40
                   constr_args.Rd:103
                   split_cols_by.Rd:59
                   split_cols_by_multivar.Rd:44
                   split_rows_by.Rd:79
                   split_rows_by_multivar.Rd:69
                   summarize_row_groups.Rd:52
                   tabclasses.Rd:113
                   varcuts.Rd:149
                   NEWS.md:76
                   clinical_trials.Rmd:686
                   introduction.Rmd:145
                   sorting_pruning.Rmd:486
Layouting          lyt_args.Rd:5,208
                   README.md:221
                   README.Rmd:161
Lewandowski        README.md:199
                   README.Rmd:146
mandatorily        NEWS.md:115,205
Maximo             README.md:199
                   README.Rmd:146
Modelling          example_analysis_coxreg.Rmd:2
multivariable      example_analysis_coxreg.Rmd:16
NSE                clinical_trials.Rmd:396
orderable          sorting_pruning.Rmd:199
Paszty             README.md:199
                   README.Rmd:146
pathing            add_combo_facet.Rd:13
                   avarspl.Rd:92
                   cutsplits.Rd:84
                   formatters_methods.Rd:211,216,227
                   lyt_args.Rd:70,101
                   MultiVarSplit.Rd:40,59
                   split_cols_by_multivar.Rd:28
                   VarLevelSplit.Rd:82
                   NEWS.md:220
                   sorting_pruning.Rmd:232,256,438
                   subsetting_tables.Rmd:195
Phuse              clinical_trials.Rmd:435
postprocessing     add_combo_facet.Rd:6,27
                   split_functions.Rmd:273
Postprocessing     make_split_fun.Rd:35,67
                   trim_levels_in_facets.Rd:5,18
pre                add_colcounts.Rd:10
                   add_existing_table.Rd:10
                   add_overall_col.Rd:10
                   analyze.Rd:24
                   analyze_colvars.Rd:18
                   append_topleft.Rd:10
                   build_table.Rd:19,51
                   custom_split_funs.Rd:25,28,98
                   int_methods.Rd:1096
                   lyt_args.Rd:55
                   make_split_fun.Rd:73
                   matrix_form-VTableTree-method.Rd:18
                   split_cols_by.Rd:21,78,81
                   split_cols_by_multivar.Rd:18
                   split_funcs.Rd:83,86
                   split_rows_by.Rd:25,105,108
                   split_rows_by_multivar.Rd:23
                   summarize_row_groups.Rd:19
                   varcuts.Rd:89
                   vil.Rd:11,34
                   NEWS.md:78
                   custom_appearance.Rmd:108
                   example_analysis_coxreg.Rmd:373
                   introduction.Rmd:138,409
                   sorting_pruning.Rmd:386
                   split_functions.Rmd:46,281,290,300,309,411
Pre                col_accessors.Rd:119
                   example_analysis_coxreg.Rmd:25
                   split_functions.Rmd:431,434,442
priori             split_functions.Rmd:151
programmatically   README.md:62
                   README.Rmd:56
Qi                 README.md:199
                   README.Rmd:146
quartiles          varcuts.Rd:152,159
reindexed          head_tail.Rd:62
repo               README.md:18,29
                   README.Rmd:29,35
repped             analyze.Rd:85
                   analyze_colvars.Rd:21
                   names.Rd:29
responder          clinical_trials.Rmd:740
Resync             NEWS.md:165
reusability        clinical_trials.Rmd:401
RinPharma          README.md:210
                   README.Rmd:153
roadmap            clinical_trials.Rmd:889
Saibah             README.md:199
                   README.Rmd:146
sortable           sorting_pruning.Rmd:438
spl                analyze.Rd:145
                   spl_context.Rd:5,7,9
                   spl_context_to_disp_path.Rd:5,17
Stoilova           README.md:199
                   README.Rmd:146
subtable           add_existing_table.Rd:16
                   analyze.Rd:63
                   analyze_colvars.Rd:39
                   avarspl.Rd:100
                   CellValue.Rd:32
                   cutsplits.Rd:97
                   int_methods.Rd:1125
                   label_at_path.Rd:27,29,31
                   lyt_args.Rd:160
                   ManualSplit.Rd:37
                   MultiVarSplit.Rd:72
                   paginate.Rd:45
                   rcell.Rd:45
                   rowclasses.Rd:60
                   split_rows_by.Rd:63
                   split_rows_by_multivar.Rd:54
                   summarize_row_groups.Rd:41
                   tabclasses.Rd:92
                   table_structure.Rd:16
                   trim_prune_funs.Rd:59,63
                   validate_table_struct.Rd:18
                   varcuts.Rd:143
                   VarLevelSplit.Rd:95
                   NEWS.md:116
                   introduction.Rmd:332
                   sorting_pruning.Rmd:30,111,119,137,199,222,232,237,290,296,344
Subtable           sorting_pruning.Rmd:288
subtable's         sorting_pruning.Rmd:207
subtables          basic_table.Rd:18,20
                   constr_args.Rd:79,81
                   find_degen_struct.Rd:13
                   horizontal_sep.Rd:29
                   paginate.Rd:97,138
                   qtable.Rd:39,41
                   sort_at_path.Rd:80
                   tabclasses.Rd:96,98
                   validate_table_struct.Rd:17
                   NEWS.md:39,114
                   introduction.Rmd:359,368
                   sorting_pruning.Rmd:28,31,102,111,191,207,237,461
Subtables          trim_prune_funs.Rd:36
summarization      tabulation_dplyr.Rmd:128,162
tableone           introduction.Rmd:36
Tadeusz            README.md:199
                   README.Rmd:146
unicode            build_table.Rd:40
                   gen_args.Rd:91
                   rtable.Rd:26
                   tabclasses.Rd:107
univariable        example_analysis_coxreg.Rmd:16
unnested           df_to_tt.Rd:13
unpruned           sorting_pruning.Rmd:147
unstratified       clinical_trials.Rmd:745
Unstratified       clinical_trials.Rmd:712
useR               README.md:224
                   README.Rmd:163
                   introduction.Rmd:55
xtable             introduction.Rmd:35
Yung               README.md:199
                   README.Rmd:146

@m7pr m7pr self-assigned this Jul 12, 2023
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
@shajoezhu
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hi @m7pr , many thanks for this, can I suggest we do the sweep right before #678? there are a few PRs are about to be merged in

@m7pr m7pr marked this pull request as ready for review July 12, 2023 18:13
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m7pr commented Jul 12, 2023

Hey @shajoezhu - I am ready with my part. I suggest we merge now, so everything that is required by #678 will already have spell-check fixed and you will only need to figure out the new spelling issues that will be triggered by GitHub Actions spelling check. I reckon it will be easier to solve future spelling issues one-by-one on a single PR than once again once multiple PRs are merged.

@m7pr m7pr requested review from shajoezhu and pawelru July 12, 2023 18:16
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Thanks, Marcin to work on this. I think we need to put it on hold merging it after #665. What you think @shajoezhu @gmbecker

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m7pr commented Jul 13, 2023

IMHO the sooner you merge, the sooner you start paying attention to spelling anywhere

vignettes/introduction.Rmd Outdated Show resolved Hide resolved
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
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Melkiades commented Jul 13, 2023

IMHO the sooner you merge, the sooner you start paying attention to spelling anywhere

Trust me, we did know very well about the problem which predates the current SME team.

Anyway, if you insist we can merge it in already, but I have the feeling that this is going to break all PRs currently open and it is not a great timing for this.

In general, we need to collaborate, and please at least warn us about it beforehand. Just let us know before starting working on these kinds of issues as it may not be the best timing for those. Also, this work is not on Kendis, and it is clearly something that has dependencies on our team.

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IMHO the sooner you merge, the sooner you start paying attention to spelling anywhere

Trust me, we did know very well about the problem which predates the current SME team.

Anyway, if you insist we can merge it in already, but I have the feeling that this is going to break all PRs currently open and it is not a great timing for this.

But this is my council: flag this on @gogonzo to liaison with @shajoezhu on the best way forward before any merge is being considered. In the interim, hold fire on this one.

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pawelru commented Jul 13, 2023

In general, we need to collaborate, and please at least warn us about it beforehand

Apologies guys. The whole blame is on me. Bad planning. I chatted with Marcin and I ask him to complete that for rtables repo. Anyway, @shajoezhu please make a call what to do with this PR. Even if it will wait - I don't expect a lot of complex git conflicts to be resolved.

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shajoezhu commented Jul 13, 2023

hey guys, thanks for working on this. I am blocking the merge for now. I would like to resolve other issues first, which are priorities for the release

@shajoezhu shajoezhu marked this pull request as draft July 13, 2023 09:53
@m7pr
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m7pr commented Jul 13, 2023

Apologies, I was not aware that there is release going on. Take your time to merge it. Flag me also when you think it can be merged and I'll fix conflicts and update files after you made changes to your PRs.

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hi @m7pr , can you add a NEWS entry please. Thanks!

m7pr added 2 commits July 14, 2023 09:19
Merge branch 'main' into update_wordlist@main

# Conflicts:
#	NEWS.md
#	R/tt_export.R
#	man/ard_specs.Rd
#	man/as_result_df.Rd
@m7pr m7pr marked this pull request as ready for review July 14, 2023 07:23
@m7pr m7pr requested a review from shajoezhu July 14, 2023 07:23
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m7pr commented Jul 14, 2023

Yes @shajoezhu - I did fix conflicts and updated NEWS with a relevant note about the spelling revision

Signed-off-by: Joe Zhu <joe.zhu@roche.com>
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badge

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/00tabletrees.R               662      46  93.05%   24, 94, 96, 371, 447-448, 451, 590, 681, 763-764, 854, 856-857, 880-881, 901, 1080-1083, 1214, 1298-1299, 1358-1361, 1394-1395, 1401-1406, 1449, 1455, 1544, 1636, 1647, 1649-1650, 1653-1654, 1682, 1708-1709
R/as_html.R                     88       7  92.05%   7-12, 68
R/colby_constructors.R         489      17  96.52%   63, 106-107, 155-156, 202-203, 328, 341, 1063, 1138, 1281, 1317, 1336, 1356, 1375, 1519
R/compare_rtables.R             78      11  85.90%   95-96, 99-100, 113-114, 131, 150-151, 181, 185
R/format_rcell.R                12       0  100.00%
R/indent.R                      13       2  84.62%   39-40
R/index_footnotes.R             52       0  100.00%
R/make_split_fun.R              97      15  84.54%   22-25, 48-49, 51-52, 103, 106, 252, 254-255, 259-260, 276, 366
R/make_subset_expr.R           106      12  88.68%   26-35, 93-98, 131, 197, 208, 215
R/simple_analysis.R              5       1  80.00%   48
R/split_funs.R                 424      54  87.26%   131, 135, 140-145, 149, 159-161, 195-196, 318-321, 337-342, 412, 452, 466-467, 481, 537, 546-547, 549, 561, 601, 621, 780, 787, 812-813, 821-822, 824-825, 983-984, 995-998, 1061-1062, 1118-1119
R/summary.R                    187      20  89.30%   40, 84, 188, 195, 260-263, 273-274, 293-294, 399, 453-457, 485, 513
R/tree_accessors.R             798      74  90.73%   93, 210, 223, 240, 271, 281, 293, 385, 407-408, 662-666, 774, 788, 805, 846, 900-901, 933, 959, 991-995, 1042, 1104-1106, 1120, 1186, 1272-1273, 1291, 1305-1306, 1314, 1344, 1357-1360, 1378-1381, 1445, 1483, 1573, 1651, 1661, 1671, 1680, 1686, 1692-1695, 1973, 2250, 2344, 2426-2432, 2576, 2675, 2698-2726, 2738-2743
R/tt_afun_utils.R              345      25  92.75%   44, 146, 152, 160-169, 218, 229-230, 452, 459-460, 524-526, 545, 559-560
R/tt_compare_tables.R           65       4  93.85%   56, 170, 248, 251
R/tt_compatibility.R           413      50  87.89%   19, 137-138, 187, 191, 321-322, 325-328, 335, 338, 365, 371-372, 442, 484, 513, 531, 555-556, 596, 609-611, 680, 705-708, 717, 769, 775, 782-783, 887, 893, 919-931, 960-961
R/tt_dotabulation.R            825      47  94.30%   36, 202, 204, 247, 268, 271-272, 318, 350-351, 372, 379-380, 460, 582-584, 633, 636, 665, 852, 855, 882, 993-994, 1149-1153, 1250, 1343-1351, 1367-1370, 1381, 1385, 1390, 1399, 1403
R/tt_export.R                  202      36  82.18%   47, 63, 104-105, 136, 175-177, 233-246, 398-399, 405, 448-454, 458-460, 556-557, 569
R/tt_from_df.R                   9       0  100.00%
R/tt_paginate.R                382      26  93.19%   47, 69, 100-105, 355, 456-457, 474-476, 619-620, 664-669, 733, 735, 744, 750, 753
R/tt_pos_and_access.R          519      37  92.87%   73, 75-76, 100, 152, 187-189, 234, 471, 473, 480, 486, 499, 508-509, 673, 684-686, 692-695, 723, 765-766, 776, 927-928, 976-1000, 1224, 1294
R/tt_showmethods.R             121      20  83.47%   47, 73-87, 138, 154-157, 163, 170, 172-174, 252-253
R/tt_sort.R                     76       3  96.05%   211-212, 218
R/tt_toString.R                325      23  92.92%   112, 305, 318, 327, 334, 336, 342-352, 435, 489, 495, 704-729
R/utils.R                       15       1  93.33%   109
R/validate_table_struct.R       75      11  85.33%   76-79, 88-89, 129, 137-138, 191-192
R/Viewer.R                      56       9  83.93%   51, 55, 65-68, 87-88, 118
TOTAL                         6439     551  91.44%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/00tabletrees.R               +38      +5  -0.38%
R/colby_constructors.R          +7       0  +0.05%
R/index_footnotes.R             +2       0  +100.00%
R/make_split_fun.R             +97     +15  +84.54%
R/split_funs.R                  +3      -1  +0.33%
R/summary.R                     +4      +4  -1.95%
R/tree_accessors.R              +5      +6  -0.70%
R/tt_dotabulation.R            +88      +3  +0.27%
R/tt_export.R                  -27     -37  +14.06%
R/tt_paginate.R                 -1     +11  -2.89%
R/tt_pos_and_access.R           -1       0  -0.01%
R/tt_showmethods.R               0      -1  +0.83%
R/tt_sort.R                     -5      -3  +3.46%
R/tt_toString.R                +20      +1  +0.14%
R/utils.R                       +4       0  +2.42%
R/validate_table_struct.R      +75     +11  +85.33%
TOTAL                         +309     +14  +0.20%

Results for commit: 04124d4

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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Unit Tests Summary

    1 files    21 suites   1m 30s ⏱️
171 tests 171 ✔️ 0 💤 0
736 runs  736 ✔️ 0 💤 0

Results for commit 675de57.

@shajoezhu shajoezhu mentioned this pull request Jul 26, 2023
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lgtm! many thanks @m7pr

@m7pr m7pr merged commit 8edc885 into main Jul 28, 2023
17 checks passed
@m7pr m7pr deleted the update_wordlist@main branch July 28, 2023 13:41
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4 participants