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1089 always avail alt df - #1102

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1089_always_avail_alt_df
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1089 always avail alt df#1102
gmbecker wants to merge 4 commits into
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1089_always_avail_alt_df

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gmbecker marked this pull request as ready for review July 31, 2026 18:24
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gmbecker requested a review from shajoezhu as a code owner July 31, 2026 18:24
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fixes #1089

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Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/00tabletrees.R               894      68  92.39%   20, 72-76, 138, 141, 472, 563-564, 567, 729, 835, 962-963, 1065, 1068, 1070-1071, 1089-1092, 1112, 1227-1230, 1328-1333, 1496, 1597-1600, 1724-1727, 1764-1767, 1773-1778, 1838, 1845, 1941, 2053, 2066, 2069-2072, 2075-2078, 2108, 2141-2142
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, 1215-1219, 1221-1225, 1306, 1395, 1556, 1595, 1606, 1614, 1617, 1642, 1663, 1809, 2032-2035
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     152  88.19%   110, 139-140, 264, 284, 310, 333, 363, 381, 400-404, 424, 446-449, 576, 603-604, 890-896, 1004, 1043, 1062, 1088, 1140, 1188-1189, 1202-1203, 1216-1217, 1262, 1297, 1335-1340, 1399, 1473-1477, 1495-1504, 1582, 1702-1705, 1730, 1752-1753, 1763, 1814, 1835-1840, 1861-1866, 2002, 2043, 2142, 2249, 2262, 2276, 2292, 2301, 2311-2315, 2365-2370, 2573, 2583-2586, 2596, 2621-2624, 2631, 2633-2636, 2758, 2792-2793, 2850, 3154, 3515, 3631, 3665-3690, 3781-3789, 3950, 4024-4030, 4335, 4459, 4544-4549, 4555, 4579-4584, 4632, 4657-4681, 4710-4716
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           1261     102  91.91%   56, 262, 267, 269, 318, 343, 347-350, 383-386, 409, 442-445, 473-476, 603-604, 672, 859-863, 913, 917, 945-948, 958, 978-982, 989-992, 1256, 1260, 1291, 1395-1398, 1604-1612, 1876-1885, 1904-1913, 1939, 1967-1970, 1981, 1986, 1991-1992, 1994, 2005, 2010, 2033, 2119-2138
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                         8997     828  90.80%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  -------
R/tt_dotabulation.R       -5      +5  -0.43%
TOTAL                     -5      +5  -0.06%

Results for commit: 406bcf9

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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Unit Tests Summary

    1 files     31 suites   1m 53s ⏱️
  253 tests   253 ✅ 0 💤 0 ❌
1 943 runs  1 943 ✅ 0 💤 0 ❌

Results for commit 406bcf9.

♻️ This comment has been updated with latest results.

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Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
Accessor tests 💚 $5.22$ $-1.04$ $0$ $0$ $0$ $0$
Exporting to txt, pdf, rtf, and docx 💚 $8.76$ $-1.44$ $0$ $0$ $0$ $0$
Tabulation framework 💚 $27.27$ $-1.44$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Content functions (cfun) 👶 $+0.13$ .alt_df_argument_behavior_is_correct_when_alt_counts_df_is_not_set

Results for commit 0135660

♻️ This comment has been updated with latest results.

Comment thread R/colby_constructors.R
#' For the `.alt_df*` family of parameters, these will be passed data
#' subsets based on `df` if no `alt_counts_df` is specified in the
#' `build_table` call. In `rtables` versions `<= 0.6.13`, this instead
#' resulted in an error. }

@Melkiades Melkiades Aug 11, 2026

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@gmbecker small thing on the version here,I checked the tags and the stop() was actually still in v0.6.16, it is only being removed in this PR. So <= 0.6.13 is not right, it should point to the last release before this fix (0.6.16) or just say "in previous versions" to be safe. Also there is a double space and the closing } got glued onto the sentence (error. }), and this paragraph is sitting inside the \describe{} block, so it will render as a weird list item. I would move it out just after the closing brace so it reads as body text.

Comment thread R/colby_constructors.R
#' `build_table` call. In `rtables` versions `<= 0.6.13`, this instead
#' resulted in an error. }
#'
#' @note If any of these formals is specified incorrectly or not present in the tabulation machinery, it will be

@Melkiades Melkiades Aug 11, 2026

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Related to the note just below (line 1056): it still says .alt_df_row and .alt_df "will not be present" when no alt_counts_df is given, but that is exactly what we are changing here, so it now contradicts the paragraph right above. Can we update/drop it? Otherwise it is a bit confusing for the user ;)

check_alt_dfs <- function(df, .df_row, .alt_df_row, .alt_df, .alt_df_full) {
expect_identical(df, .alt_df)
expect_identical(.df_row, .alt_df_row)
expect_false(is.null(.alt_df_full))

@Melkiades Melkiades Aug 11, 2026

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Nice test. One thing, here we only check .alt_df_full is not NULL, but the whole point is that it is the full df (not the row-group subset). I would add an expect_identical(.alt_df_full, ex_adsl) like the existing "full alt_counts_df is accessible" test does, otherwise a regression where it collapses to the subset would still pass here.

expect_error(lyt |> build_table(DM),
regexp = "Layout contains afun\\/cfun functions that have optional*"
)

@Melkiades Melkiades Aug 11, 2026

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Minor leftover: removing the old expect_error left a dangling blank line here, the keep_levels comment now floats away from the build_table call it refers to. Just yo tidy up.

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2 participants