Direct formatted output from `as_result_df` #793

Melkiades · 2023-11-28T14:08:34Z

addition of as_strings, as_viewer, and expand_colnames for what I imagine is easier QCing. @kieranjmartin fyi

@mrmorgan17 try it out. Options are described in ?as_result_df

Fixes #784

Melkiades · 2023-11-28T14:10:32Z

DESCRIPTION

@@ -34,13 +34,13 @@ Depends:
    methods,
    R (>= 2.10)
 Imports:
+    checkmate (>= 2.1.0),


I think it is time @edelarua @shajoezhu

Melkiades · 2023-11-28T14:11:13Z

R/tt_export.R

+  cellvals <- as.data.frame(do.call(rbind, raw_cvals))
+  row.names(cellvals) <- NULL
+
+  if (as_viewer || as_strings) {


core of changes

Melkiades · 2023-11-28T14:11:24Z

R/tt_export.R

+  )
+
+  # If we want to expand colnames
+  if (expand_colnames) {


github-actions · 2023-11-28T14:16:08Z

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/00tabletrees.R               744      62  91.67%   21, 102, 105, 412, 496-497, 500, 656, 757, 849-850, 951, 953-954, 977-980, 1002, 1114-1117, 1212-1217, 1365, 1462-1465, 1529-1532, 1568-1571, 1577-1582, 1632, 1639, 1739, 1852, 1866, 1869-1872, 1875-1878, 1906, 1937-1938
R/as_html.R                    161      25  84.47%   5-10, 74, 131-136, 141-146, 161-165, 253
R/colby_constructors.R         558      20  96.42%   71, 123, 181-184, 244-247, 387, 404, 1213, 1306, 1468, 1506, 1528, 1552, 1573, 1729
R/compare_rtables.R             83      17  79.52%   93-96, 99-102, 115-118, 137, 157-158, 189, 194
R/format_rcell.R                12       0  100.00%
R/indent.R                      13       2  84.62%   39-40
R/index_footnotes.R             66       0  100.00%
R/make_split_fun.R             119      23  80.67%   22-25, 51-54, 57-60, 115, 119, 280, 283-286, 291-294, 313, 412
R/make_subset_expr.R           136      14  89.71%   34-48, 126-133, 168, 250, 266, 274
R/simple_analysis.R              5       1  80.00%   55
R/split_funs.R                 505      66  86.93%   143, 148, 154-159, 164, 181-185, 366-371, 388-393, 474, 526, 544-547, 564, 631, 641-642, 644, 658, 702, 727, 903, 910, 936-939, 950-951, 953, 955, 1126-1128, 1142-1146, 1210-1213, 1276-1279
R/summary.R                    215      24  88.84%   38, 85, 192, 200, 271-276, 287-288, 307-308, 418, 465-481, 516, 549
R/tree_accessors.R             946     102  89.22%   109, 251, 269, 292, 330, 344, 360, 465, 492-493, 774-779, 907, 925, 949, 999, 1054-1055, 1094, 1127, 1163-1167, 1220, 1295-1299, 1317-1327, 1396, 1501-1504, 1529, 1549-1550, 1559, 1600, 1618-1622, 1643-1647, 1726, 1768, 1872, 1976, 1989, 2002, 2016, 2024, 2033-2037, 2379, 2737, 2850, 2883-2905, 2994-3001, 3156, 3229-3234, 3443-3444, 3451, 3454-3457, 3461, 3512, 3546, 3571-3595
R/tt_afun_utils.R              411      32  92.21%   50, 164, 171, 181-194, 260, 271-272, 504, 512-515, 597-601, 622, 637-639
R/tt_compare_tables.R           70       4  94.29%   56, 178, 257, 261
R/tt_compatibility.R           510      56  89.02%   19, 142-143, 192, 197, 332-333, 337-340, 346, 350, 398, 520, 568, 601, 621, 654-657, 701, 718-722, 809, 837-840, 849, 912, 920, 931-934, 1044, 1051, 1080-1094, 1125-1126
R/tt_dotabulation.R           1117      96  91.41%   54, 252, 257, 259, 310, 334, 338-341, 373-376, 399, 434-437, 465-468, 565, 702-706, 756, 760, 789-792, 802, 822-826, 833-836, 1095, 1099, 1130, 1243-1246, 1442-1450, 1591, 1675-1684, 1764-1767, 1778, 1783, 1788-1789, 1791, 1802, 1807, 1830, 1925-1944
R/tt_export.R                  540      39  92.78%   44, 173-177, 216-219, 261-264, 316-320, 384, 438, 524-527, 542, 886, 895, 920-924, 1091-1094, 1097, 1128, 1134
R/tt_from_df.R                   9       0  100.00%
R/tt_paginate.R                440      37  91.59%   45, 70, 107-115, 396, 518-521, 541-545, 695-698, 748-755, 824, 827, 837, 844, 847
R/tt_pos_and_access.R          571      43  92.47%   77, 79-81, 106, 166, 212-216, 262, 514, 516, 524, 530, 544, 554-557, 739, 750-754, 759-762, 789, 842-843, 855, 1021-1022, 1080-1108, 1388, 1465
R/tt_showmethods.R             144      21  85.42%   60, 97-120, 183, 209, 218, 226, 229-233, 326-327
R/tt_sort.R                     88       5  94.32%   223-226, 234
R/tt_toString.R                395      25  93.67%   115, 306, 356, 371, 381, 388, 391, 397-407, 495, 560, 566, 801-827
R/utils.R                       29       0  100.00%
R/validate_table_struct.R       84      10  88.10%   79-83, 92-93, 140, 150-151
R/Viewer.R                      61       9  85.25%   47, 51, 61-65, 85, 119
TOTAL                         8032     733  90.87%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/00tabletrees.R              +120     +21  -1.76%
R/as_html.R                    +73     +18  -7.57%
R/colby_constructors.R         +76      +3  -0.06%
R/compare_rtables.R             +5      +6  -6.38%
R/index_footnotes.R            +16       0  +100.00%
R/make_split_fun.R            +119     +23  +80.67%
R/make_subset_expr.R           +30      +2  +1.03%
R/split_funs.R                 +84     +11  -0.01%
R/summary.R                    +32      +8  -2.42%
R/tree_accessors.R            +153     +34  -2.21%
R/tt_afun_utils.R              +66      +7  -0.54%
R/tt_compare_tables.R           +5       0  +0.44%
R/tt_compatibility.R           +97      +6  +1.13%
R/tt_dotabulation.R           +380     +52  -2.62%
R/tt_export.R                 +311     -34  +24.66%
R/tt_paginate.R                +57     +22  -4.49%
R/tt_pos_and_access.R          +51      +6  -0.42%
R/tt_showmethods.R             +23       0  +2.77%
R/tt_sort.R                     +7      -1  +1.73%
R/tt_toString.R                +90      +3  +0.88%
R/utils.R                      +18      -1  +9.09%
R/validate_table_struct.R      +84     +10  +88.10%
R/Viewer.R                      +5       0  +1.32%
TOTAL                        +1902    +196  -0.37%

Results for commit: 9a53fd7

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-11-28T14:17:09Z

Unit Tests Summary

      1 files     24 suites 1m 27s ⏱️
  196 tests   196 ✔️ 0 💤 0 ❌
1 504 runs 1 504 ✔️ 0 💤 0 ❌

Results for commit 9a53fd7.

♻️ This comment has been updated with latest results.

…es into 784_direct_as_result_df@main

edelarua · 2023-11-28T19:33:22Z

Hi @Melkiades,

Looks great so far! Thanks for working on this as I think it's much needed :)

One thing I noticed - when there are mixed numeric types (i.e. integers & doubles) in a single column, the integers are converted to NAs. I know you can't mix types in a data frame column, so would it be possible to instead convert the integers to doubles, which I feel would be more practical? It works fine if as_strings = TRUE but I would assume this would often be useful in the as_strings = FALSE case as well to extract values.

Example:

lyt <- basic_table() %>%
    split_cols_by("ARM") %>%
    split_rows_by("STRATA1") %>%
    analyze(c("AGE", "BMRKR2"))

tbl <- build_table(lyt, ex_adsl)
as_result_df(tbl, simplify = TRUE, as_viewer = TRUE)

   row_name A: Drug X B: Placebo C: Combination
1      Mean     33.08      35.11          34.23
2       LOW        NA         NA             NA
3    MEDIUM        NA         NA             NA
4      HIGH        NA         NA             NA
5      Mean     33.85         36          36.33
6       LOW        NA         NA             NA
7    MEDIUM        NA         NA             NA
8      HIGH        NA         NA             NA
9      Mean     34.22      35.18          35.63
10      LOW        NA         NA             NA
11   MEDIUM        NA         NA             NA
12     HIGH        NA         NA             NA

Melkiades · 2023-11-28T20:16:36Z

Thanks, @edelarua, for finding this problem at the source! It should be fixed now ;)

edelarua · 2023-11-28T22:46:55Z

Thanks, @edelarua, for finding this problem at the source! It should be fixed now ;)

Perfect! It's all working for me now. You may want to wait for feedback from others but if not I think it's good to go :)

Melkiades added 3 commits November 28, 2023 11:49

better docs

2b18a77

order and addition of features on top of v0_experimental

9cf72b8

expanded tests

2781a77

Melkiades added enhancement sme labels Nov 28, 2023

Melkiades requested review from edelarua and ayogasekaram as code owners November 28, 2023 14:08

Merge branch 'main' into 784_direct_as_result_df@main

0f3257d

Melkiades commented Nov 28, 2023

View reviewed changes

R/tt_export.R

)

# If we want to expand colnames

if (expand_colnames) {

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and here

Melkiades added 6 commits November 28, 2023 15:54

fixes

62d299e

news

2be3123

Merge branch '784_direct_as_result_df@main' of github.com:Roche/rtabl…

1cabafb

…es into 784_direct_as_result_df@main

styling

cb0db2e

adding stringi

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news

6afbf55

integer fix

9a53fd7

edelarua approved these changes Nov 28, 2023

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Melkiades merged commit c4018e7 into main Nov 29, 2023
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Melkiades deleted the 784_direct_as_result_df@main branch November 29, 2023 08:55

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Direct formatted output from `as_result_df` #793

Direct formatted output from `as_result_df` #793

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Direct formatted output from as_result_df #793

Direct formatted output from as_result_df #793

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Direct formatted output from `as_result_df` #793

Direct formatted output from `as_result_df` #793

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