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jkniziajknizia
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Fix test
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+49
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‎R/fda-table_35.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -197,10 +197,10 @@ make_table_35_rtables <- function(df,
197197
) |>
198198
append_topleft(c("", lbl_soc_var))
199199

200-
tbl <- build_table(lyt, df = adae, alt_counts_df = alt_counts_df) |>
200+
tbl <- build_table(lyt, df = df, alt_counts_df = alt_counts_df) |>
201201
sort_at_path(
202202
path = c(soc_var),
203-
scorefun = score_occurrences_cols(col_names = levels(adae[[arm_var]]))
203+
scorefun = score_occurrences_cols(col_names = levels(df[[arm_var]]))
204204
)
205205
if (prune_0) tbl <- prune_table(tbl)
206206

‎tests/testthat/_snaps/fda-table_35.md

+47-42
Original file line numberDiff line numberDiff line change
@@ -3,66 +3,70 @@
33
Code
44
as.data.frame(res$table)
55
Output
6-
row_type var_label variable label stat_1 stat_2 stat_3
7-
1 level <br /> AEBODSYS cl A.1 78 (59.1) 75 (57.7) 89 (55.6)
8-
2 level <br /> AEBODSYS cl B.1 47 (83.9) 49 (81.7) 43 (69.4)
9-
3 level <br /> AEBODSYS cl B.2 79 (61.2) 74 (53.6) 85 (59.4)
10-
4 level <br /> AEBODSYS cl C.1 43 (78.2) 46 (73.0) 43 (67.2)
11-
5 level <br /> AEBODSYS cl C.2 35 (72.9) 48 (90.6) 55 (84.6)
12-
6 level <br /> AEBODSYS cl D.1 79 (62.2) 67 (63.2) 80 (59.3)
13-
7 level <br /> AEBODSYS cl D.2 47 (75.8) 58 (80.6) 57 (77.0)
6+
**System Organ Class** **A: Drug X** \nN = 609 **B: Placebo** \nN = 622 **C: Combination** \nN = 703
7+
1 cl A.1 78 (59%) 75 (58%) 89 (56%)
8+
2 cl B.1 47 (84%) 49 (82%) 43 (69%)
9+
3 cl B.2 79 (61%) 74 (54%) 85 (59%)
10+
4 cl C.1 43 (78%) 46 (73%) 43 (67%)
11+
5 cl C.2 35 (73%) 48 (91%) 55 (85%)
12+
6 cl D.1 79 (62%) 67 (63%) 80 (59%)
13+
7 cl D.2 47 (76%) 58 (81%) 57 (77%)
1414

1515
---
1616

1717
Code
1818
res$ard
19+
Output
20+
$tbl_hierarchical
1921
Message
20-
{cards} data frame: 72 x 11
22+
{cards} data frame: 72 x 13
2123
Output
22-
group1 group1_level variable variable_level stat_name stat_label stat
23-
1 ARM A: Drug X AEBODSYS cl A.1 n n 78
24-
2 ARM A: Drug X AEBODSYS cl A.1 N N 132
25-
3 ARM A: Drug X AEBODSYS cl A.1 p % 0.591
26-
4 ARM A: Drug X AEBODSYS cl B.1 n n 47
27-
5 ARM A: Drug X AEBODSYS cl B.1 N N 56
28-
6 ARM A: Drug X AEBODSYS cl B.1 p % 0.839
29-
7 ARM A: Drug X AEBODSYS cl B.2 n n 79
30-
8 ARM A: Drug X AEBODSYS cl B.2 N N 129
31-
9 ARM A: Drug X AEBODSYS cl B.2 p % 0.612
32-
10 ARM A: Drug X AEBODSYS cl C.1 n n 43
24+
group1 group1_level variable variable_level stat_name stat_label stat stat_fmt
25+
1 ARM A: Drug X AEBODSYS cl A.1 n n 78 78
26+
2 ARM A: Drug X AEBODSYS cl A.1 N N 132 132
27+
3 ARM A: Drug X AEBODSYS cl A.1 p % 0.591 59
28+
4 ARM A: Drug X AEBODSYS cl B.1 n n 47 47
29+
5 ARM A: Drug X AEBODSYS cl B.1 N N 56 56
30+
6 ARM A: Drug X AEBODSYS cl B.1 p % 0.839 84
31+
7 ARM A: Drug X AEBODSYS cl B.2 n n 79 79
32+
8 ARM A: Drug X AEBODSYS cl B.2 N N 129 129
33+
9 ARM A: Drug X AEBODSYS cl B.2 p % 0.612 61
34+
10 ARM A: Drug X AEBODSYS cl C.1 n n 43 43
3335
Message
3436
i 62 more rows
3537
i Use `print(n = ...)` to see more rows
36-
i 4 more variables: context, fmt_fn, warning, error
38+
i 5 more variables: context, fmt_fn, warning, error, gts_column
39+
Output
40+
3741

3842
# Table 35 generation works with gtsummary with custom values
3943

4044
Code
4145
as.data.frame(res)
4246
Output
43-
row_type var_label variable label stat_1 stat_2 stat_3
44-
1 level <br /> AEBODSYS cl A.1 78 (58.2) 75 (56.0) 89 (67.4)
45-
2 level <br /> AEBODSYS cl B.1 47 (35.1) 49 (36.6) 43 (32.6)
46-
3 level <br /> AEBODSYS cl B.2 79 (59.0) 74 (55.2) 85 (64.4)
47-
4 level <br /> AEBODSYS cl C.1 43 (32.1) 46 (34.3) 43 (32.6)
48-
5 level <br /> AEBODSYS cl C.2 35 (26.1) 48 (35.8) 55 (41.7)
49-
6 level <br /> AEBODSYS cl D.1 79 (59.0) 67 (50.0) 80 (60.6)
50-
7 level <br /> AEBODSYS cl D.2 47 (35.1) 58 (43.3) 57 (43.2)
47+
**System Organ Class** **A: Drug X** \nN = 134 **B: Placebo** \nN = 134 **C: Combination** \nN = 132
48+
1 cl A.1 78 (58%) 75 (56%) 89 (67%)
49+
2 cl B.1 47 (35%) 49 (37%) 43 (33%)
50+
3 cl B.2 79 (59%) 74 (55%) 85 (64%)
51+
4 cl C.1 43 (32%) 46 (34%) 43 (33%)
52+
5 cl C.2 35 (26%) 48 (36%) 55 (42%)
53+
6 cl D.1 79 (59%) 67 (50%) 80 (61%)
54+
7 cl D.2 47 (35%) 58 (43%) 57 (43%)
5155

5256
# Table 35 generation works with gtsummary missing values
5357

5458
Code
5559
as.data.frame(res)
5660
Output
57-
row_type var_label variable label stat_1 stat_2 stat_3
58-
1 level <br /> AEBODSYS cl A.1 78 (58.2) 75 (56.0) 89 (67.4)
59-
2 level <br /> AEBODSYS cl B.1 47 (35.1) 49 (36.6) 43 (32.6)
60-
3 level <br /> AEBODSYS cl B.2 79 (59.0) 74 (55.2) 84 (63.6)
61-
4 level <br /> AEBODSYS cl C.1 43 (32.1) 46 (34.3) 42 (31.8)
62-
5 level <br /> AEBODSYS cl C.2 34 (25.4) 48 (35.8) 55 (41.7)
63-
6 level <br /> AEBODSYS cl D.1 79 (59.0) 67 (50.0) 79 (59.8)
64-
7 level <br /> AEBODSYS cl D.2 47 (35.1) 58 (43.3) 57 (43.2)
65-
8 level <br /> AEBODSYS &lt;Missing&gt; 2 (1.5) 2 (1.5) 6 (4.5)
61+
**System Organ Class** **A: Drug X** \nN = 134 **B: Placebo** \nN = 134 **C: Combination** \nN = 132
62+
1 cl A.1 78 (58%) 75 (56%) 89 (67%)
63+
2 cl B.1 47 (35%) 49 (37%) 43 (33%)
64+
3 cl B.2 79 (59%) 74 (55%) 84 (64%)
65+
4 cl C.1 43 (32%) 46 (34%) 42 (32%)
66+
5 cl C.2 34 (25%) 48 (36%) 55 (42%)
67+
6 cl D.1 79 (59%) 67 (50%) 79 (60%)
68+
7 cl D.2 47 (35%) 58 (43%) 57 (43%)
69+
8 <Missing> 2 (1.5%) 2 (1.5%) 6 (4.5%)
6670

6771
# Table 35 generation works with custom values
6872

@@ -123,12 +127,13 @@
123127
Body System or Organ Class (N=134) (N=134) (N=132)
124128
—————————————————————————————————————————————————————————————————————
125129
cl A.1 78 (58.2%) 75 (56.0%) 89 (67.4%)
126-
cl B.2 79 (59.0%) 74 (55.2%) 85 (64.4%)
127-
cl D.1 79 (59.0%) 67 (50.0%) 80 (60.6%)
130+
cl B.2 79 (59.0%) 74 (55.2%) 84 (63.6%)
131+
cl D.1 79 (59.0%) 67 (50.0%) 79 (59.8%)
128132
cl D.2 47 (35.1%) 58 (43.3%) 57 (43.2%)
129133
cl B.1 47 (35.1%) 49 (36.6%) 43 (32.6%)
130-
cl C.2 35 (26.1%) 48 (35.8%) 55 (41.7%)
131-
cl C.1 43 (32.1%) 46 (34.3%) 43 (32.6%)
134+
cl C.2 34 (25.4%) 48 (35.8%) 55 (41.7%)
135+
cl C.1 43 (32.1%) 46 (34.3%) 42 (31.8%)
136+
<Missing> 2 (1.5%) 2 (1.5%) 6 (4.5%)
132137

133138
# Table 35 generation works with custom values (SOC variable and label)
134139

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