Add guided advanced vignettes

[gmbecker]

and needed fixes/utilities for them

[Melkiades]

Repeated entry

[gmbecker]

Thats weird, as it wasn't manually added, but I'll look into this

[Melkiades]

Duplicated with the above. I guess it should be:
setMethod("obj_na_str", "RowsVerticalSection", function(obj) attr(obj, "row_na_strs", exact = TRUE))

[gmbecker]

correct nice catch. thanks

[Melkiades]

This would return NULL. why should it? Could you add a comment and maybe a more explicit NULL value?

[gmbecker]

This is missing code not intended to return NULL so I'll either remove it (if its not needed) or fix it.

Nice catch thanks.

[Melkiades]

I would use vapply(lst, inherits, logical(1), "RowsVerticalSection") as it is a expected logical

[Melkiades]

68 new words is a lot. Some look like they could be R object names or code fragments that should be in backticks in the vignettes rather than whitelisted (e.g., afun, afuns, bbbs, splfun). Worth checking if wrapping them in backticks in the Rmd files removes the need for the wordlist entries

[gmbecker]

will look into this,s ome of those are real (bbbs stands for Behavioral Building Blocks, which is a term I use heavily in one of the vignettes to refer to the functions we pass to pre and post in make_split_fun, others do look like variable names though

[Melkiades]

This is probably the right behavior, but it should be documented in NEWS since it changes the semantics of the setter

[gmbecker]

this is a bugfix rather than a semantics change because if you give it a single value something down stream (printing, I think) breaks, but still worth putting in the NEWS file

[Melkiades]

Thanks Gabe for the PR!! I added a couple of comments ^^

In general, I would suggest to add link to the issue and add the NEWS file when ready to review. If possible I would do bug fixes and docs improvement in different PRs, but it is not an issue

[gmbecker]

Sorry @Melkiades this probably should have been marked as a draft, but thanks for going through it and I will go through all your comments and respond to each (and likely make most suggested changes)

[github-actions]

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/00tabletrees.R               894      89  90.04%   20, 72-76, 114, 117, 448, 539-540, 543, 705, 811, 938-939, 1041, 1044, 1046-1047, 1065-1068, 1088, 1203-1206, 1304-1309, 1472, 1573-1576, 1700-1703, 1740-1743, 1749-1754, 1814, 1821, 1917, 2029, 2042, 2045-2048, 2051-2054, 2084, 2117-2118, 2194-2219
R/as_html.R                    172      25  85.47%   5-10, 80, 152-157, 162-167, 182-186, 273
R/colby_constructors.R         626      36  94.25%   81, 134, 197-200, 267-270, 411, 427, 1211-1215, 1217-1221, 1302, 1391, 1552, 1591, 1602, 1610, 1613, 1638, 1659, 1805, 2028-2031
R/compare_rtables.R             83      17  79.52%   93-96, 99-102, 115-118, 137, 156-157, 188, 193
R/custom_split_funs.R          265      40  84.91%   127, 132, 138-143, 156, 173-177, 353-358, 375-380, 456, 502, 518-521, 537, 599, 609-610, 612, 624, 668, 693
R/default_split_funs.R         287      22  92.33%   272, 335-338, 349-350, 352, 354, 551-555, 619-622, 685-688
R/format_rcell.R                17       1  94.12%   47
R/indent.R                      13       2  84.62%   40-41
R/index_footnotes.R             66       0  100.00%
R/make_split_fun.R             166      30  81.93%   22-26, 36-39, 52-55, 58-61, 115, 119, 267, 270-273, 278-281, 366, 375, 377, 379, 430
R/make_subset_expr.R           137      14  89.78%   77-92, 169-177, 213, 302, 306, 315
R/summary.R                    144      38  73.61%   35, 80, 178-220, 269, 315-331, 366, 397
R/tree_accessors.R            1287     154  88.03%   110, 139-140, 264, 284, 310, 333, 363, 381, 400-404, 424, 446-449, 576, 603-604, 890-896, 1004, 1043, 1062, 1088, 1140, 1161, 1188-1189, 1202-1203, 1216-1217, 1226, 1262, 1297, 1335-1340, 1399, 1473-1477, 1495-1504, 1582, 1702-1705, 1730, 1752-1753, 1763, 1814, 1835-1840, 1861-1866, 1951, 1992, 2091, 2198, 2211, 2225, 2241, 2250, 2260-2264, 2314-2319, 2522, 2532-2535, 2545, 2570-2573, 2580, 2582-2585, 2707, 2741-2742, 2799, 3103, 3464, 3580, 3614-3639, 3730-3738, 3899, 3973-3979, 4284, 4408, 4493-4498, 4504, 4528-4533, 4581, 4606-4630, 4659-4665
R/tt_afun_utils.R              419      33  92.12%   60, 182, 189, 198-212, 280, 288-289, 507, 515-518, 600-604, 624, 638-640
R/tt_as_df.R                   400      23  94.25%   101-104, 112, 150, 224-227, 369, 388, 458, 477-480, 489, 599, 605, 637, 655, 707
R/tt_compare_tables.R           72       4  94.44%   51, 174, 249, 253
R/tt_compatibility.R           574      70  87.80%   22, 149-150, 193, 198, 329-330, 334-337, 343, 347, 531, 585-588, 625-627, 665, 698, 718, 738-741, 751-754, 799, 816-820, 826-829, 903, 930-933, 942, 1004, 1012, 1023-1026, 1137, 1144, 1172-1186, 1217-1218
R/tt_dotabulation.R           1266      97  92.34%   60, 255, 260, 262, 311, 336, 340-343, 376-379, 402, 435-438, 466-469, 596-597, 665, 852-856, 906, 910, 938-941, 951, 971-975, 982-985, 1249, 1253, 1284, 1388-1391, 1605-1613, 1877-1886, 1968-1971, 1982, 1987, 1992-1993, 1995, 2006, 2011, 2034, 2120-2139
R/tt_export.R                   13       1  92.31%   45
R/tt_from_df.R                  15       0  100.00%
R/tt_paginate.R                535      40  92.52%   74, 122-131, 242, 341-342, 494, 629-632, 653-657, 802-805, 856-863, 940, 943, 961, 968, 971
R/tt_pos_and_access.R          656      33  94.97%   76, 78-80, 105, 166, 262, 329, 438, 512, 516, 724, 726, 734, 740, 754, 764-767, 990, 1007-1010, 1037, 1096-1097, 1110, 1346-1347, 1373-1376, 1658, 1733
R/tt_showmethods.R             162      21  87.04%   56, 91-113, 223, 249, 258, 263, 266-270, 359-360
R/tt_sort.R                    115       6  94.78%   50, 289-292, 300
R/tt_toString.R                439      24  94.53%   125, 355, 377, 390, 400, 406, 409, 415-425, 518, 619, 826-851
R/utils.R                       34       7  79.41%   56, 169-174
R/validate_table_struct.R       84      10  88.10%   80-84, 93-94, 140, 149-150
R/Viewer.R                      61       9  85.25%   46, 50, 60-64, 84, 118
TOTAL                         9002     846  90.60%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/00tabletrees.R        +21     +21  -2.17%
R/tree_accessors.R       +7      +7  -0.48%
TOTAL                   +28     +28  -0.28%

Results for commit: ddde119

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files     30 suites   1m 57s ⏱️
  249 tests   249 ✅ 0 💤 0 ❌
1 856 runs  1 856 ✅ 0 💤 0 ❌

Results for commit ddde119.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
Pagination	💔	$17.25$	$+1.11$	$0$	$0$	$0$	$0$
Result Data Frames	💔	$11.16$	$+1.12$	$0$	$0$	$0$	$0$
Tabulation framework	💔	$23.86$	$+1.91$	$0$	$0$	$0$	$0$

Results for commit 5809237

♻️ This comment has been updated with latest results.

[gmbecker]

superceded by #1093 I believe all of the review comments here have been addressed with the current state there.