tests/testthat/_snaps/tbl_hierarchical.md
In ddsjoberg/gtsummary: Presentation-Ready Data Summary and Analytic Result Tables
tbl_hierarchical(data) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = trt, denominator = trial2,
id = id))
Output
**Chemotherapy Treatment** **N = 200**
1 Drug A 45 (46%)
2 Drug B 44 (43%)
Code
tbl_hierarchical()
Condition
Error in `tbl_hierarchical()`:
! The `data` argument cannot be missing.
Code
tbl_hierarchical(data = letters)
Condition
Error in `tbl_hierarchical()`:
! The `data` argument must be class <data.frame>, not a character vector.
tbl_hierarchical(by) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = stage, by = trt,
denominator = trial2, id = id))
Condition
Warning:
Duplicate rows found in data for the "id" column.
i Percentages/Denominators are not correct.
Output
**T Stage** **Drug A** \nN = 98 **Drug B** \nN = 102
1 T1 22 (79%) 22 (88%)
2 T2 20 (80%) 22 (76%)
3 T3 20 (91%) 18 (86%)
4 T4 21 (91%) 21 (78%)
Code
tbl_hierarchical(data = trial2, variables = stage, by = name, denominator = trial2,
id = id)
Condition
Error in `tbl_hierarchical()`:
! Error processing `by` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", "ttdeath", and "id"
tbl_hierarchical(id) works properly
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = 10)
Condition
Error in `tbl_hierarchical()`:
! Error processing `id` argument.
! Can't select columns past the end. i Location 10 doesn't exist. i There are only 9 columns.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", "ttdeath", and "id"
tbl_hierarchical(denominator) works properly
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = "test", id = id)
Condition
Error in `tbl_hierarchical()`:
! The `denominator` argument must be a <data.frame> or an <integer>, not a string.
tbl_hierarchical(include) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade),
denominator = trial2, id = id, include = grade))
Output
**T Stage** \n **Grade** **N = 200**
1 T1 <NA>
2 I 14 (82%)
3 II 20 (87%)
4 III 12 (92%)
5 T2 <NA>
6 I 16 (89%)
7 II 15 (88%)
8 III 17 (89%)
9 T3 <NA>
10 I 16 (89%)
11 II 9 (82%)
12 III 14 (100%)
13 T4 <NA>
14 I 14 (93%)
15 II 14 (82%)
16 III 18 (100%)
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade), by = trt,
denominator = trial2, id = id, include = NULL))
Condition
Warning:
Duplicate rows found in data for the "id" column.
i Percentages/Denominators are not correct.
Output
**T Stage** \n **Grade** **Drug A** \nN = 98 **Drug B** \nN = 102
1 T1 <NA> <NA>
2 I 7 (88%) 8 (89%)
3 II 12 (86%) 9 (100%)
4 III 6 (100%) 6 (86%)
5 T2 <NA> <NA>
6 I 7 (88%) 10 (100%)
7 II 8 (100%) 7 (78%)
8 III 8 (89%) 9 (90%)
9 T3 <NA> <NA>
10 I 10 (91%) 7 (100%)
11 II 5 (100%) 6 (100%)
12 III 6 (100%) 8 (100%)
13 T4 <NA> <NA>
14 I 8 (100%) 7 (100%)
15 II 5 (100%) 10 (83%)
16 III 10 (100%) 8 (100%)
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, include = name)
Condition
Error in `tbl_hierarchical()`:
! Error processing `include` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "stage" and "grade"
tbl_hierarchical(statistic) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade),
denominator = trial2, id = id, statistic = ~"{n}, {N}, {p}"))
Output
**T Stage** \n **Grade** **N = 200**
1 T1 36, 53, 68
2 I 14, 17, 82
3 II 20, 23, 87
4 III 12, 13, 92
5 T2 37, 54, 69
6 I 16, 18, 89
7 II 15, 17, 88
8 III 17, 19, 89
9 T3 32, 43, 74
10 I 16, 18, 89
11 II 9, 11, 82
12 III 14, 14, 100
13 T4 35, 50, 70
14 I 14, 15, 93
15 II 14, 17, 82
16 III 18, 18, 100
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, statistic = ~ list(stage = "{n}"))
Condition
Error in `tbl_hierarchical()`:
! Values passed in the `statistic` argument must be strings with glue elements containing one or more of "n", "N", and "p".
tbl_hierarchical(overall_row) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = id, overall_row = TRUE))
Output
**Chemotherapy Treatment** **N = 200**
1 Number of patients with event 50 (25%)
2 Drug A 45 (46%)
3 Drug B 44 (43%)
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **I** \nN = 68 **II** \nN = 68 **III** \nN = 64
1 Number of patients with event 40 (59%) 38 (56%) 39 (61%)
2 Drug A 25 (71%) 27 (84%) 23 (74%)
3 Drug B 24 (73%) 26 (72%) 26 (79%)
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = id, overall_row = "test")
Condition
Error in `tbl_hierarchical()`:
! The `overall_row` argument must be class <logical>, not a string.
tbl_hierarchical(label) works properly
Code
as.data.frame(res)
Output
**My Stage** \n **My Grade** **N = 200**
1 T1 36 (68%)
2 I 14 (82%)
3 II 20 (87%)
4 III 12 (92%)
5 T2 37 (69%)
6 I 16 (89%)
7 II 15 (88%)
8 III 17 (89%)
9 T3 32 (74%)
10 I 16 (89%)
11 II 9 (82%)
12 III 14 (100%)
13 T4 35 (70%)
14 I 14 (93%)
15 II 14 (82%)
16 III 18 (100%)
"**My Stage** \n **My Grade**"
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, label = "Stages")
Condition
Error in `internal_tbl_hierarchical()`:
! The `label` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical(digits) works properly
Code
as.data.frame(res)
Output
**T Stage** \n **Grade** **N = 200**
1 T1 36 (68%)
2 I 14,0 (82.353%)
3 II 20,0 (86.957%)
4 III 12,0 (92.308%)
5 T2 37 (69%)
6 I 16,0 (88.889%)
7 II 15,0 (88.235%)
8 III 17,0 (89.474%)
9 T3 32 (74%)
10 I 16,0 (88.889%)
11 II 9,0 (81.818%)
12 III 14,0 (100.000%)
13 T4 35 (70%)
14 I 14,0 (93.333%)
15 II 14,0 (82.353%)
16 III 18,0 (100.000%)
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, digits = "0")
Condition
Error in `internal_tbl_hierarchical()`:
! The `digits` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical works properly when last variable of hierarchy is ordered
Code
as.data.frame(res_o)
Output
**Primary System Organ Class** \n **Highest Severity**
1 CARDIAC DISORDERS
2 MILD
3 MODERATE
4 SEVERE
5 GASTROINTESTINAL DISORDERS
6 MILD
7 MODERATE
8 SEVERE
9 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS
10 MILD
11 MODERATE
12 SEVERE
13 INFECTIONS AND INFESTATIONS
14 MILD
15 MODERATE
16 SEVERE
17 SKIN AND SUBCUTANEOUS TISSUE DISORDERS
18 MILD
19 MODERATE
20 SEVERE
**Placebo** \nN = 86 **Xanomeline High Dose** \nN = 84
1 <NA> <NA>
2 2 (2.3%) 1 (1.2%)
3 0 (0%) 2 (2.4%)
4 1 (1.2%) 0 (0%)
5 <NA> <NA>
6 9 (10%) 2 (2.4%)
7 1 (1.2%) 2 (2.4%)
8 0 (0%) 0 (0%)
9 <NA> <NA>
10 8 (9.3%) 15 (18%)
11 1 (1.2%) 13 (15%)
12 0 (0%) 0 (0%)
13 <NA> <NA>
14 4 (4.7%) 2 (2.4%)
15 2 (2.3%) 1 (1.2%)
16 0 (0%) 0 (0%)
17 <NA> <NA>
18 5 (5.8%) 11 (13%)
19 4 (4.7%) 4 (4.8%)
20 0 (0%) 0 (0%)
**Xanomeline Low Dose** \nN = 84
1 <NA>
2 0 (0%)
3 0 (0%)
4 0 (0%)
5 <NA>
6 5 (6.0%)
7 0 (0%)
8 0 (0%)
9 <NA>
10 14 (17%)
11 11 (13%)
12 2 (2.4%)
13 <NA>
14 1 (1.2%)
15 0 (0%)
16 0 (0%)
17 <NA>
18 6 (7.1%)
19 9 (11%)
20 0 (0%)
Code
as.data.frame(res)
Output
**Primary System Organ Class** \n **AESEV** **N = 254**
1 CARDIAC DISORDERS 6 (2.4%)
2 MILD 3 (1.2%)
3 MODERATE 2 (0.8%)
4 SEVERE 1 (0.4%)
5 GASTROINTESTINAL DISORDERS 19 (7.5%)
6 MILD 16 (6.3%)
7 MODERATE 3 (1.2%)
8 SEVERE 0 (0%)
9 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 64 (25%)
10 MILD 37 (15%)
11 MODERATE 25 (9.8%)
12 SEVERE 2 (0.8%)
13 INFECTIONS AND INFESTATIONS 10 (3.9%)
14 MILD 7 (2.8%)
15 MODERATE 3 (1.2%)
16 SEVERE 0 (0%)
17 SKIN AND SUBCUTANEOUS TISSUE DISORDERS 39 (15%)
18 MILD 22 (8.7%)
19 MODERATE 17 (6.7%)
20 SEVERE 0 (0%)
tbl_hierarchical_count(data) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = trt))
Output
**Chemotherapy Treatment** Overall
1 Drug A 98
2 Drug B 102
Code
as.data.frame(tbl_hierarchical_count(data = iris, variables = Species))
Output
**Species** Overall
1 setosa 50
2 versicolor 50
3 virginica 50
Code
tbl_hierarchical_count()
Condition
Error in `tbl_hierarchical_count()`:
! The `data` argument cannot be missing.
Code
tbl_hierarchical_count(data = letters)
Condition
Error in `tbl_hierarchical_count()`:
! The `data` argument must be class <data.frame>, not a character vector.
tbl_hierarchical_count(by) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = stage, by = trt))
Output
**T Stage** **Drug A** **Drug B**
1 T1 28 25
2 T2 25 29
3 T3 22 21
4 T4 23 27
Code
tbl_hierarchical_count(data = trial, variables = stage, by = name)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `by` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", and "ttdeath"
tbl_hierarchical_count(denominator) works properly
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **N = 400**
1 Drug A 98
2 Drug B 102
Code
tbl_hierarchical_count(data = trial, variables = trt, denominator = "test")
Condition
Error in `tbl_hierarchical_count()`:
! The `denominator` argument must be empty, a <data.frame>, or an <integer>, not a string.
tbl_hierarchical_count(include) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = c(stage, grade),
include = grade))
Output
**T Stage** \n **Grade** Overall
1 T1 <NA>
2 I 17
3 II 23
4 III 13
5 T2 <NA>
6 I 18
7 II 17
8 III 19
9 T3 <NA>
10 I 18
11 II 11
12 III 14
13 T4 <NA>
14 I 15
15 II 17
16 III 18
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = c(stage, grade),
by = trt, include = NULL))
Output
**T Stage** \n **Grade** **Drug A** **Drug B**
1 T1 <NA> <NA>
2 I 8 9
3 II 14 9
4 III 6 7
5 T2 <NA> <NA>
6 I 8 10
7 II 8 9
8 III 9 10
9 T3 <NA> <NA>
10 I 11 7
11 II 5 6
12 III 6 8
13 T4 <NA> <NA>
14 I 8 7
15 II 5 12
16 III 10 8
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), include = name)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `include` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "stage" and "grade"
tbl_hierarchical_count(overall_row) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = trt,
overall_row = TRUE))
Output
**Chemotherapy Treatment** Overall
1 Total number of events 200
2 Drug A 98
3 Drug B 102
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **I** **II** **III**
1 Total number of events 68 68 64
2 Drug A 35 32 31
3 Drug B 33 36 33
Code
tbl_hierarchical_count(data = trial, variables = trt, overall_row = "test")
Condition
Error in `tbl_hierarchical_count()`:
! The `overall_row` argument must be class <logical>, not a string.
tbl_hierarchical_count(label) works properly
Code
as.data.frame(res)
Output
**My Stage** \n **My Grade** Overall
1 T1 53
2 I 17
3 II 23
4 III 13
5 T2 54
6 I 18
7 II 17
8 III 19
9 T3 43
10 I 18
11 II 11
12 III 14
13 T4 50
14 I 15
15 II 17
16 III 18
"**My Stage** \n **My Grade**"
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), label = "Stages")
Condition
Error in `internal_tbl_hierarchical()`:
! The `label` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical_count(digits) works properly
Code
as.data.frame(res)
Output
**T Stage** \n **Grade** Overall
1 T1 53,0
2 I 17,0
3 II 23,0
4 III 13,0
5 T2 54,0
6 I 18,0
7 II 17,0
8 III 19,0
9 T3 43,0
10 I 18,0
11 II 11,0
12 III 14,0
13 T4 50,0
14 I 15,0
15 II 17,0
16 III 18,0
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), digits = n ~
2)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `digits` argument.
! Can't select columns that don't exist. x Column `n` doesn't exist.
i Select among columns "stage", "grade", and "..ard_hierarchical_overall.."
tbl_hierarchical_count with 10+ hierarchy variables
Code
as.data.frame(res)
Output
**x1** \n **x2** \n **x3** \n **x4** \n **x5** \n **x6** \n **x7** \n **x8** \n **x9** \n ...
1 A
2 C
3 E
4 H
5 I
6 K
7 N
8 O
9 Q
10 S
11 J
12 K
13 M
14 P
15 Q
16 S
17 L
18 M
19 P
20 R
21 T
22 F
23 G
24 I
25 K
26 N
27 O
28 Q
29 S
30 L
31 M
32 O
33 R
34 S
35 P
36 R
37 T
38 H
39 I
40 K
41 M
42 O
43 Q
44 S
45 J
46 L
47 N
48 P
49 R
50 T
51 D
52 E
53 G
54 I
55 L
56 M
57 O
58 Q
59 T
60 N
61 P
62 Q
63 T
64 J
65 K
66 N
67 P
68 Q
69 T
70 L
71 N
72 O
73 R
74 T
75 H
76 I
77 L
78 N
79 P
80 R
81 T
82 J
83 K
84 N
85 O
86 Q
87 T
88 F
89 G
90 I
91 L
92 N
93 O
94 Q
95 T
96 J
97 K
98 N
99 O
100 R
101 S
102 L
103 M
104 P
105 Q
106 S
107 H
108 I
109 K
110 M
111 P
112 Q
113 T
114 R
115 T
116 N
117 P
118 R
119 T
120 B
121 C
122 E
123 G
124 J
125 K
126 M
127 O
128 Q
129 T
130 F
131 G
132 J
133 K
134 M
135 O
136 Q
137 S
138 H
139 I
140 K
141 M
142 P
143 R
144 T
145 D
146 E
147 H
148 J
149 K
150 N
151 O
152 Q
153 T
154 L
155 M
156 P
157 Q
158 T
159 F
160 G
161 I
162 K
163 N
164 O
165 Q
166 T
167 L
168 M
169 O
170 R
171 T
172 J
173 K
174 M
175 O
176 R
177 T
178 L
179 M
180 P
181 R
182 T
183 H
184 J
185 L
186 N
187 P
188 Q
189 T
Overall
1 <NA>
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 <NA>
10 1
11 <NA>
12 <NA>
13 <NA>
14 <NA>
15 <NA>
16 1
17 <NA>
18 <NA>
19 <NA>
20 <NA>
21 1
22 <NA>
23 <NA>
24 <NA>
25 <NA>
26 <NA>
27 <NA>
28 <NA>
29 1
30 <NA>
31 <NA>
32 <NA>
33 <NA>
34 1
35 <NA>
36 <NA>
37 1
38 <NA>
39 <NA>
40 <NA>
41 <NA>
42 <NA>
43 <NA>
44 1
45 <NA>
46 <NA>
47 <NA>
48 <NA>
49 <NA>
50 1
51 <NA>
52 <NA>
53 <NA>
54 <NA>
55 <NA>
56 <NA>
57 <NA>
58 <NA>
59 1
60 <NA>
61 <NA>
62 <NA>
63 1
64 <NA>
65 <NA>
66 <NA>
67 <NA>
68 <NA>
69 1
70 <NA>
71 <NA>
72 <NA>
73 <NA>
74 1
75 <NA>
76 <NA>
77 <NA>
78 <NA>
79 <NA>
80 <NA>
81 1
82 <NA>
83 <NA>
84 <NA>
85 <NA>
86 <NA>
87 1
88 <NA>
89 <NA>
90 <NA>
91 <NA>
92 <NA>
93 <NA>
94 <NA>
95 1
96 <NA>
97 <NA>
98 <NA>
99 <NA>
100 <NA>
101 1
102 <NA>
103 <NA>
104 <NA>
105 <NA>
106 1
107 <NA>
108 <NA>
109 <NA>
110 <NA>
111 <NA>
112 <NA>
113 1
114 <NA>
115 1
116 <NA>
117 <NA>
118 <NA>
119 1
120 <NA>
121 <NA>
122 <NA>
123 <NA>
124 <NA>
125 <NA>
126 <NA>
127 <NA>
128 <NA>
129 1
130 <NA>
131 <NA>
132 <NA>
133 <NA>
134 <NA>
135 <NA>
136 <NA>
137 1
138 <NA>
139 <NA>
140 <NA>
141 <NA>
142 <NA>
143 <NA>
144 1
145 <NA>
146 <NA>
147 <NA>
148 <NA>
149 <NA>
150 <NA>
151 <NA>
152 <NA>
153 1
154 <NA>
155 <NA>
156 <NA>
157 <NA>
158 1
159 <NA>
160 <NA>
161 <NA>
162 <NA>
163 <NA>
164 <NA>
165 <NA>
166 1
167 <NA>
168 <NA>
169 <NA>
170 <NA>
171 1
172 <NA>
173 <NA>
174 <NA>
175 <NA>
176 <NA>
177 1
178 <NA>
179 <NA>
180 <NA>
181 <NA>
182 1
183 <NA>
184 <NA>
185 <NA>
186 <NA>
187 <NA>
188 <NA>
189 1
tbl_hierarchical_count table_body enables sorting
Code
res$table_body
Output
# A tibble: 21 x 11
row_type group1 group1_level group2 group2_level var_label variable label stat_1 stat_2 stat_3
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 level ..ard_hierarchical_overall.. <NA> <NA> <NA> <NA> ..ard_hierarchical_overall.. Number of patients with event 26 (30%) 42 (50%) 40 (48%)
2 level SEX F <NA> <NA> <NA> SEX F 13 (25%) 18 (45%) 23 (46%)
3 level SEX F AESOC CARDIAC DISORDERS <NA> AESOC CARDIAC DISORDERS 0 (0%) 1 (2.5%) 0 (0%)
4 level SEX F AESOC CARDIAC DISORDERS <NA> AETERM ATRIOVENTRICULAR BLOCK SECOND DEGREE 0 (0%) 1 (2.5%) 0 (0%)
5 level SEX F AESOC GASTROINTESTINAL DISORDERS <NA> AESOC GASTROINTESTINAL DISORDERS 3 (5.7%) 0 (0%) 3 (6.0%)
6 level SEX F AESOC GASTROINTESTINAL DISORDERS <NA> AETERM DIARRHOEA 3 (5.7%) 0 (0%) 3 (6.0%)
7 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 5 (9.4%) 11 (28%) 13 (26%)
8 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AETERM APPLICATION SITE ERYTHEMA 2 (3.8%) 5 (13%) 5 (10%)
9 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AETERM APPLICATION SITE PRURITUS 4 (7.5%) 10 (25%) 12 (24%)
10 level SEX F AESOC SKIN AND SUBCUTANEOUS TISSUE DISORDERS <NA> AESOC SKIN AND SUBCUTANEOUS TISSUE DISORDERS 6 (11%) 7 (18%) 9 (18%)
# i 11 more rows
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tbl_hierarchical(data) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = trt, denominator = trial2,
id = id))
Output
**Chemotherapy Treatment** **N = 200**
1 Drug A 45 (46%)
2 Drug B 44 (43%)
Code
tbl_hierarchical()
Condition
Error in `tbl_hierarchical()`:
! The `data` argument cannot be missing.
Code
tbl_hierarchical(data = letters)
Condition
Error in `tbl_hierarchical()`:
! The `data` argument must be class <data.frame>, not a character vector.
tbl_hierarchical(by) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = stage, by = trt,
denominator = trial2, id = id))
Condition
Warning:
Duplicate rows found in data for the "id" column.
i Percentages/Denominators are not correct.
Output
**T Stage** **Drug A** \nN = 98 **Drug B** \nN = 102
1 T1 22 (79%) 22 (88%)
2 T2 20 (80%) 22 (76%)
3 T3 20 (91%) 18 (86%)
4 T4 21 (91%) 21 (78%)
Code
tbl_hierarchical(data = trial2, variables = stage, by = name, denominator = trial2,
id = id)
Condition
Error in `tbl_hierarchical()`:
! Error processing `by` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", "ttdeath", and "id"
tbl_hierarchical(id) works properly
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = 10)
Condition
Error in `tbl_hierarchical()`:
! Error processing `id` argument.
! Can't select columns past the end. i Location 10 doesn't exist. i There are only 9 columns.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", "ttdeath", and "id"
tbl_hierarchical(denominator) works properly
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = "test", id = id)
Condition
Error in `tbl_hierarchical()`:
! The `denominator` argument must be a <data.frame> or an <integer>, not a string.
tbl_hierarchical(include) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade),
denominator = trial2, id = id, include = grade))
Output
**T Stage** \n **Grade** **N = 200**
1 T1 <NA>
2 I 14 (82%)
3 II 20 (87%)
4 III 12 (92%)
5 T2 <NA>
6 I 16 (89%)
7 II 15 (88%)
8 III 17 (89%)
9 T3 <NA>
10 I 16 (89%)
11 II 9 (82%)
12 III 14 (100%)
13 T4 <NA>
14 I 14 (93%)
15 II 14 (82%)
16 III 18 (100%)
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade), by = trt,
denominator = trial2, id = id, include = NULL))
Condition
Warning:
Duplicate rows found in data for the "id" column.
i Percentages/Denominators are not correct.
Output
**T Stage** \n **Grade** **Drug A** \nN = 98 **Drug B** \nN = 102
1 T1 <NA> <NA>
2 I 7 (88%) 8 (89%)
3 II 12 (86%) 9 (100%)
4 III 6 (100%) 6 (86%)
5 T2 <NA> <NA>
6 I 7 (88%) 10 (100%)
7 II 8 (100%) 7 (78%)
8 III 8 (89%) 9 (90%)
9 T3 <NA> <NA>
10 I 10 (91%) 7 (100%)
11 II 5 (100%) 6 (100%)
12 III 6 (100%) 8 (100%)
13 T4 <NA> <NA>
14 I 8 (100%) 7 (100%)
15 II 5 (100%) 10 (83%)
16 III 10 (100%) 8 (100%)
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, include = name)
Condition
Error in `tbl_hierarchical()`:
! Error processing `include` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "stage" and "grade"
tbl_hierarchical(statistic) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = c(stage, grade),
denominator = trial2, id = id, statistic = ~"{n}, {N}, {p}"))
Output
**T Stage** \n **Grade** **N = 200**
1 T1 36, 53, 68
2 I 14, 17, 82
3 II 20, 23, 87
4 III 12, 13, 92
5 T2 37, 54, 69
6 I 16, 18, 89
7 II 15, 17, 88
8 III 17, 19, 89
9 T3 32, 43, 74
10 I 16, 18, 89
11 II 9, 11, 82
12 III 14, 14, 100
13 T4 35, 50, 70
14 I 14, 15, 93
15 II 14, 17, 82
16 III 18, 18, 100
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, statistic = ~ list(stage = "{n}"))
Condition
Error in `tbl_hierarchical()`:
! Values passed in the `statistic` argument must be strings with glue elements containing one or more of "n", "N", and "p".
tbl_hierarchical(overall_row) works properly
Code
as.data.frame(tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = id, overall_row = TRUE))
Output
**Chemotherapy Treatment** **N = 200**
1 Number of patients with event 50 (25%)
2 Drug A 45 (46%)
3 Drug B 44 (43%)
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **I** \nN = 68 **II** \nN = 68 **III** \nN = 64
1 Number of patients with event 40 (59%) 38 (56%) 39 (61%)
2 Drug A 25 (71%) 27 (84%) 23 (74%)
3 Drug B 24 (73%) 26 (72%) 26 (79%)
Code
tbl_hierarchical(data = trial2, variables = trt, denominator = trial2, id = id, overall_row = "test")
Condition
Error in `tbl_hierarchical()`:
! The `overall_row` argument must be class <logical>, not a string.
tbl_hierarchical(label) works properly
Code
as.data.frame(res)
Output
**My Stage** \n **My Grade** **N = 200**
1 T1 36 (68%)
2 I 14 (82%)
3 II 20 (87%)
4 III 12 (92%)
5 T2 37 (69%)
6 I 16 (89%)
7 II 15 (88%)
8 III 17 (89%)
9 T3 32 (74%)
10 I 16 (89%)
11 II 9 (82%)
12 III 14 (100%)
13 T4 35 (70%)
14 I 14 (93%)
15 II 14 (82%)
16 III 18 (100%)
"**My Stage** \n **My Grade**"
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, label = "Stages")
Condition
Error in `internal_tbl_hierarchical()`:
! The `label` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical(digits) works properly
Code
as.data.frame(res)
Output
**T Stage** \n **Grade** **N = 200**
1 T1 36 (68%)
2 I 14,0 (82.353%)
3 II 20,0 (86.957%)
4 III 12,0 (92.308%)
5 T2 37 (69%)
6 I 16,0 (88.889%)
7 II 15,0 (88.235%)
8 III 17,0 (89.474%)
9 T3 32 (74%)
10 I 16,0 (88.889%)
11 II 9,0 (81.818%)
12 III 14,0 (100.000%)
13 T4 35 (70%)
14 I 14,0 (93.333%)
15 II 14,0 (82.353%)
16 III 18,0 (100.000%)
Code
tbl_hierarchical(data = trial2, variables = c(stage, grade), denominator = trial2,
id = id, digits = "0")
Condition
Error in `internal_tbl_hierarchical()`:
! The `digits` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical works properly when last variable of hierarchy is ordered
Code
as.data.frame(res_o)
Output
**Primary System Organ Class** \n **Highest Severity**
1 CARDIAC DISORDERS
2 MILD
3 MODERATE
4 SEVERE
5 GASTROINTESTINAL DISORDERS
6 MILD
7 MODERATE
8 SEVERE
9 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS
10 MILD
11 MODERATE
12 SEVERE
13 INFECTIONS AND INFESTATIONS
14 MILD
15 MODERATE
16 SEVERE
17 SKIN AND SUBCUTANEOUS TISSUE DISORDERS
18 MILD
19 MODERATE
20 SEVERE
**Placebo** \nN = 86 **Xanomeline High Dose** \nN = 84
1 <NA> <NA>
2 2 (2.3%) 1 (1.2%)
3 0 (0%) 2 (2.4%)
4 1 (1.2%) 0 (0%)
5 <NA> <NA>
6 9 (10%) 2 (2.4%)
7 1 (1.2%) 2 (2.4%)
8 0 (0%) 0 (0%)
9 <NA> <NA>
10 8 (9.3%) 15 (18%)
11 1 (1.2%) 13 (15%)
12 0 (0%) 0 (0%)
13 <NA> <NA>
14 4 (4.7%) 2 (2.4%)
15 2 (2.3%) 1 (1.2%)
16 0 (0%) 0 (0%)
17 <NA> <NA>
18 5 (5.8%) 11 (13%)
19 4 (4.7%) 4 (4.8%)
20 0 (0%) 0 (0%)
**Xanomeline Low Dose** \nN = 84
1 <NA>
2 0 (0%)
3 0 (0%)
4 0 (0%)
5 <NA>
6 5 (6.0%)
7 0 (0%)
8 0 (0%)
9 <NA>
10 14 (17%)
11 11 (13%)
12 2 (2.4%)
13 <NA>
14 1 (1.2%)
15 0 (0%)
16 0 (0%)
17 <NA>
18 6 (7.1%)
19 9 (11%)
20 0 (0%)
Code
as.data.frame(res)
Output
**Primary System Organ Class** \n **AESEV** **N = 254**
1 CARDIAC DISORDERS 6 (2.4%)
2 MILD 3 (1.2%)
3 MODERATE 2 (0.8%)
4 SEVERE 1 (0.4%)
5 GASTROINTESTINAL DISORDERS 19 (7.5%)
6 MILD 16 (6.3%)
7 MODERATE 3 (1.2%)
8 SEVERE 0 (0%)
9 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 64 (25%)
10 MILD 37 (15%)
11 MODERATE 25 (9.8%)
12 SEVERE 2 (0.8%)
13 INFECTIONS AND INFESTATIONS 10 (3.9%)
14 MILD 7 (2.8%)
15 MODERATE 3 (1.2%)
16 SEVERE 0 (0%)
17 SKIN AND SUBCUTANEOUS TISSUE DISORDERS 39 (15%)
18 MILD 22 (8.7%)
19 MODERATE 17 (6.7%)
20 SEVERE 0 (0%)
tbl_hierarchical_count(data) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = trt))
Output
**Chemotherapy Treatment** Overall
1 Drug A 98
2 Drug B 102
Code
as.data.frame(tbl_hierarchical_count(data = iris, variables = Species))
Output
**Species** Overall
1 setosa 50
2 versicolor 50
3 virginica 50
Code
tbl_hierarchical_count()
Condition
Error in `tbl_hierarchical_count()`:
! The `data` argument cannot be missing.
Code
tbl_hierarchical_count(data = letters)
Condition
Error in `tbl_hierarchical_count()`:
! The `data` argument must be class <data.frame>, not a character vector.
tbl_hierarchical_count(by) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = stage, by = trt))
Output
**T Stage** **Drug A** **Drug B**
1 T1 28 25
2 T2 25 29
3 T3 22 21
4 T4 23 27
Code
tbl_hierarchical_count(data = trial, variables = stage, by = name)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `by` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "trt", "age", "marker", "stage", "grade", "response", "death", and "ttdeath"
tbl_hierarchical_count(denominator) works properly
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **N = 400**
1 Drug A 98
2 Drug B 102
Code
tbl_hierarchical_count(data = trial, variables = trt, denominator = "test")
Condition
Error in `tbl_hierarchical_count()`:
! The `denominator` argument must be empty, a <data.frame>, or an <integer>, not a string.
tbl_hierarchical_count(include) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = c(stage, grade),
include = grade))
Output
**T Stage** \n **Grade** Overall
1 T1 <NA>
2 I 17
3 II 23
4 III 13
5 T2 <NA>
6 I 18
7 II 17
8 III 19
9 T3 <NA>
10 I 18
11 II 11
12 III 14
13 T4 <NA>
14 I 15
15 II 17
16 III 18
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = c(stage, grade),
by = trt, include = NULL))
Output
**T Stage** \n **Grade** **Drug A** **Drug B**
1 T1 <NA> <NA>
2 I 8 9
3 II 14 9
4 III 6 7
5 T2 <NA> <NA>
6 I 8 10
7 II 8 9
8 III 9 10
9 T3 <NA> <NA>
10 I 11 7
11 II 5 6
12 III 6 8
13 T4 <NA> <NA>
14 I 8 7
15 II 5 12
16 III 10 8
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), include = name)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `include` argument.
! Can't select columns that don't exist. x Column `name` doesn't exist.
i Select among columns "stage" and "grade"
tbl_hierarchical_count(overall_row) works properly
Code
as.data.frame(tbl_hierarchical_count(data = trial, variables = trt,
overall_row = TRUE))
Output
**Chemotherapy Treatment** Overall
1 Total number of events 200
2 Drug A 98
3 Drug B 102
Code
as.data.frame(res)
Output
**Chemotherapy Treatment** **I** **II** **III**
1 Total number of events 68 68 64
2 Drug A 35 32 31
3 Drug B 33 36 33
Code
tbl_hierarchical_count(data = trial, variables = trt, overall_row = "test")
Condition
Error in `tbl_hierarchical_count()`:
! The `overall_row` argument must be class <logical>, not a string.
tbl_hierarchical_count(label) works properly
Code
as.data.frame(res)
Output
**My Stage** \n **My Grade** Overall
1 T1 53
2 I 17
3 II 23
4 III 13
5 T2 54
6 I 18
7 II 17
8 III 19
9 T3 43
10 I 18
11 II 11
12 III 14
13 T4 50
14 I 15
15 II 17
16 III 18
"**My Stage** \n **My Grade**"
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), label = "Stages")
Condition
Error in `internal_tbl_hierarchical()`:
! The `label` argument must be a named list, list of formulas, a single formula, or empty.
i Review ?syntax (`?cards::syntax()`) for examples and details.
tbl_hierarchical_count(digits) works properly
Code
as.data.frame(res)
Output
**T Stage** \n **Grade** Overall
1 T1 53,0
2 I 17,0
3 II 23,0
4 III 13,0
5 T2 54,0
6 I 18,0
7 II 17,0
8 III 19,0
9 T3 43,0
10 I 18,0
11 II 11,0
12 III 14,0
13 T4 50,0
14 I 15,0
15 II 17,0
16 III 18,0
Code
tbl_hierarchical_count(data = trial, variables = c(stage, grade), digits = n ~
2)
Condition
Error in `tbl_hierarchical_count()`:
! Error processing `digits` argument.
! Can't select columns that don't exist. x Column `n` doesn't exist.
i Select among columns "stage", "grade", and "..ard_hierarchical_overall.."
tbl_hierarchical_count with 10+ hierarchy variables
Code
as.data.frame(res)
Output
**x1** \n **x2** \n **x3** \n **x4** \n **x5** \n **x6** \n **x7** \n **x8** \n **x9** \n ...
1 A
2 C
3 E
4 H
5 I
6 K
7 N
8 O
9 Q
10 S
11 J
12 K
13 M
14 P
15 Q
16 S
17 L
18 M
19 P
20 R
21 T
22 F
23 G
24 I
25 K
26 N
27 O
28 Q
29 S
30 L
31 M
32 O
33 R
34 S
35 P
36 R
37 T
38 H
39 I
40 K
41 M
42 O
43 Q
44 S
45 J
46 L
47 N
48 P
49 R
50 T
51 D
52 E
53 G
54 I
55 L
56 M
57 O
58 Q
59 T
60 N
61 P
62 Q
63 T
64 J
65 K
66 N
67 P
68 Q
69 T
70 L
71 N
72 O
73 R
74 T
75 H
76 I
77 L
78 N
79 P
80 R
81 T
82 J
83 K
84 N
85 O
86 Q
87 T
88 F
89 G
90 I
91 L
92 N
93 O
94 Q
95 T
96 J
97 K
98 N
99 O
100 R
101 S
102 L
103 M
104 P
105 Q
106 S
107 H
108 I
109 K
110 M
111 P
112 Q
113 T
114 R
115 T
116 N
117 P
118 R
119 T
120 B
121 C
122 E
123 G
124 J
125 K
126 M
127 O
128 Q
129 T
130 F
131 G
132 J
133 K
134 M
135 O
136 Q
137 S
138 H
139 I
140 K
141 M
142 P
143 R
144 T
145 D
146 E
147 H
148 J
149 K
150 N
151 O
152 Q
153 T
154 L
155 M
156 P
157 Q
158 T
159 F
160 G
161 I
162 K
163 N
164 O
165 Q
166 T
167 L
168 M
169 O
170 R
171 T
172 J
173 K
174 M
175 O
176 R
177 T
178 L
179 M
180 P
181 R
182 T
183 H
184 J
185 L
186 N
187 P
188 Q
189 T
Overall
1 <NA>
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 <NA>
10 1
11 <NA>
12 <NA>
13 <NA>
14 <NA>
15 <NA>
16 1
17 <NA>
18 <NA>
19 <NA>
20 <NA>
21 1
22 <NA>
23 <NA>
24 <NA>
25 <NA>
26 <NA>
27 <NA>
28 <NA>
29 1
30 <NA>
31 <NA>
32 <NA>
33 <NA>
34 1
35 <NA>
36 <NA>
37 1
38 <NA>
39 <NA>
40 <NA>
41 <NA>
42 <NA>
43 <NA>
44 1
45 <NA>
46 <NA>
47 <NA>
48 <NA>
49 <NA>
50 1
51 <NA>
52 <NA>
53 <NA>
54 <NA>
55 <NA>
56 <NA>
57 <NA>
58 <NA>
59 1
60 <NA>
61 <NA>
62 <NA>
63 1
64 <NA>
65 <NA>
66 <NA>
67 <NA>
68 <NA>
69 1
70 <NA>
71 <NA>
72 <NA>
73 <NA>
74 1
75 <NA>
76 <NA>
77 <NA>
78 <NA>
79 <NA>
80 <NA>
81 1
82 <NA>
83 <NA>
84 <NA>
85 <NA>
86 <NA>
87 1
88 <NA>
89 <NA>
90 <NA>
91 <NA>
92 <NA>
93 <NA>
94 <NA>
95 1
96 <NA>
97 <NA>
98 <NA>
99 <NA>
100 <NA>
101 1
102 <NA>
103 <NA>
104 <NA>
105 <NA>
106 1
107 <NA>
108 <NA>
109 <NA>
110 <NA>
111 <NA>
112 <NA>
113 1
114 <NA>
115 1
116 <NA>
117 <NA>
118 <NA>
119 1
120 <NA>
121 <NA>
122 <NA>
123 <NA>
124 <NA>
125 <NA>
126 <NA>
127 <NA>
128 <NA>
129 1
130 <NA>
131 <NA>
132 <NA>
133 <NA>
134 <NA>
135 <NA>
136 <NA>
137 1
138 <NA>
139 <NA>
140 <NA>
141 <NA>
142 <NA>
143 <NA>
144 1
145 <NA>
146 <NA>
147 <NA>
148 <NA>
149 <NA>
150 <NA>
151 <NA>
152 <NA>
153 1
154 <NA>
155 <NA>
156 <NA>
157 <NA>
158 1
159 <NA>
160 <NA>
161 <NA>
162 <NA>
163 <NA>
164 <NA>
165 <NA>
166 1
167 <NA>
168 <NA>
169 <NA>
170 <NA>
171 1
172 <NA>
173 <NA>
174 <NA>
175 <NA>
176 <NA>
177 1
178 <NA>
179 <NA>
180 <NA>
181 <NA>
182 1
183 <NA>
184 <NA>
185 <NA>
186 <NA>
187 <NA>
188 <NA>
189 1
tbl_hierarchical_count table_body enables sorting
Code
res$table_body
Output
# A tibble: 21 x 11
row_type group1 group1_level group2 group2_level var_label variable label stat_1 stat_2 stat_3
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 level ..ard_hierarchical_overall.. <NA> <NA> <NA> <NA> ..ard_hierarchical_overall.. Number of patients with event 26 (30%) 42 (50%) 40 (48%)
2 level SEX F <NA> <NA> <NA> SEX F 13 (25%) 18 (45%) 23 (46%)
3 level SEX F AESOC CARDIAC DISORDERS <NA> AESOC CARDIAC DISORDERS 0 (0%) 1 (2.5%) 0 (0%)
4 level SEX F AESOC CARDIAC DISORDERS <NA> AETERM ATRIOVENTRICULAR BLOCK SECOND DEGREE 0 (0%) 1 (2.5%) 0 (0%)
5 level SEX F AESOC GASTROINTESTINAL DISORDERS <NA> AESOC GASTROINTESTINAL DISORDERS 3 (5.7%) 0 (0%) 3 (6.0%)
6 level SEX F AESOC GASTROINTESTINAL DISORDERS <NA> AETERM DIARRHOEA 3 (5.7%) 0 (0%) 3 (6.0%)
7 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 5 (9.4%) 11 (28%) 13 (26%)
8 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AETERM APPLICATION SITE ERYTHEMA 2 (3.8%) 5 (13%) 5 (10%)
9 level SEX F AESOC GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> AETERM APPLICATION SITE PRURITUS 4 (7.5%) 10 (25%) 12 (24%)
10 level SEX F AESOC SKIN AND SUBCUTANEOUS TISSUE DISORDERS <NA> AESOC SKIN AND SUBCUTANEOUS TISSUE DISORDERS 6 (11%) 7 (18%) 9 (18%)
# i 11 more rows
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