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tests/testthat/_snaps/tbl_hierarchical_rate_by_grade.md
In crane: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
tbl_hierarchical_rate_by_grade() works
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
3 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
4 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
5 4 1 (1.2%) 0 2 (2.4%)
6 CARDIAC DISORDERS <NA> <NA> <NA>
7 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
8 1 1 (1.2%) 1 (1.2%) 0
9 2 0 2 (2.4%) 0
10 4 1 (1.2%) 0 0
11 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
12 1 1 (1.2%) 1 (1.2%) 0
13 2 0 2 (2.4%) 0
14 4 1 (1.2%) 0 0
15 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
16 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
17 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
18 2 0 2 (2.4%) 0
19 DIARRHOEA - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
20 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
21 2 0 2 (2.4%) 0
22 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> <NA> <NA>
23 - Overall - - Any Grade - 8 (9.3%) 25 (29.8%) 24 (28.6%)
24 1 7 (8.1%) 12 (14.3%) 12 (14.3%)
25 2 0 4 (4.8%) 4 (4.8%)
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 Grade 1-2 22 (25.6%) 32 (38.1%) 30 (35.7%)
3 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
4 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
5 Grade 3-4 4 (4.7%) 10 (11.9%) 10 (11.9%)
6 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
7 4 1 (1.2%) 0 2 (2.4%)
8 CARDIAC DISORDERS <NA> <NA> <NA>
9 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
10 Grade 1-2 1 (1.2%) 3 (3.6%) 0
11 1 1 (1.2%) 1 (1.2%) 0
12 2 0 2 (2.4%) 0
13 Grade 3-4 1 (1.2%) 0 0
14 4 1 (1.2%) 0 0
15 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
16 Grade 1-2 1 (1.2%) 3 (3.6%) 0
17 1 1 (1.2%) 1 (1.2%) 0
18 2 0 2 (2.4%) 0
19 Grade 3-4 1 (1.2%) 0 0
20 4 1 (1.2%) 0 0
21 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
22 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
23 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
24 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
25 2 0 2 (2.4%) 0
Code
as.data.frame(tbl)[1, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26,0/86, 30.233% 42,0/84, 50.000% 40,0/84, 47.619%
tbl_hierarchical_rate_by_grade(include_overall) works
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 Grade 1-2 22 (25.6%) 32 (38.1%) 30 (35.7%)
3 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
4 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
5 Grade 3-4 4 (4.7%) 10 (11.9%) 10 (11.9%)
6 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
7 4 1 (1.2%) 0 2 (2.4%)
8 CARDIAC DISORDERS <NA> <NA> <NA>
9 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
10 Grade 1-2 1 (1.2%) 3 (3.6%) 0
11 1 1 (1.2%) 1 (1.2%) 0
12 2 0 2 (2.4%) 0
13 Grade 3-4 1 (1.2%) 0 0
14 4 1 (1.2%) 0 0
15 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
16 Grade 1-2 1 (1.2%) 3 (3.6%) 0
17 1 1 (1.2%) 1 (1.2%) 0
18 2 0 2 (2.4%) 0
19 Grade 3-4 1 (1.2%) 0 0
20 4 1 (1.2%) 0 0
21 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
22 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
23 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
24 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
25 2 0 2 (2.4%) 0
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 CARDIAC DISORDERS <NA> <NA> <NA>
2 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
3 Grade 1-2 1 (1.2%) 3 (3.6%) 0
4 1 1 (1.2%) 1 (1.2%) 0
5 2 0 2 (2.4%) 0
6 Grade 3-4 1 (1.2%) 0 0
7 4 1 (1.2%) 0 0
8 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
9 DIARRHOEA - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
10 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
11 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
12 2 0 2 (2.4%) 0
13 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> <NA> <NA>
14 APPLICATION SITE ERYTHEMA - Any Grade - 3 (3.5%) 15 (17.9%) 12 (14.3%)
15 Grade 1-2 3 (3.5%) 12 (14.3%) 7 (8.3%)
16 1 3 (3.5%) 9 (10.7%) 4 (4.8%)
17 2 0 3 (3.6%) 3 (3.6%)
18 Grade 3-4 0 3 (3.6%) 5 (6.0%)
19 3 0 3 (3.6%) 3 (3.6%)
20 4 0 0 2 (2.4%)
21 APPLICATION SITE PRURITUS - Any Grade - 6 (7.0%) 22 (26.2%) 22 (26.2%)
22 Grade 1-2 5 (5.8%) 15 (17.9%) 17 (20.2%)
23 1 5 (5.8%) 10 (11.9%) 13 (15.5%)
24 2 0 5 (6.0%) 4 (4.8%)
25 Grade 3-4 1 (1.2%) 7 (8.3%) 5 (6.0%)
tbl_hierarchical_rate_by_grade() error messaging works
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grades_exclude = 4:5)
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! The `grades_exclude` argument must be class <character> or empty, not an integer vector.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grade_groups = list("Grade 5" ~ "5"))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade groups must be specified via a named list where each list element is a character vector of the grades to include in the grade group and each name is the corresponding name of the grade group. For example, `"Grade 3-4" = c("3", "4")`.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grade_groups = list(`Grade 3-4` = c("3", "4"), `Grade 4-5` = c("4", "5")))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade groups specified via `grade_groups` cannot overlap. Please ensure that each grade is included in at most one grade group.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grades_exclude = as.character(c(1:3, 5:7)))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade(s) "6" and "7" supplied to `grades_exclude` are invalid. All grades specified via `grades_exclude` must be levels of "AETOXGR".
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tbl_hierarchical_rate_by_grade() works
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
3 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
4 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
5 4 1 (1.2%) 0 2 (2.4%)
6 CARDIAC DISORDERS <NA> <NA> <NA>
7 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
8 1 1 (1.2%) 1 (1.2%) 0
9 2 0 2 (2.4%) 0
10 4 1 (1.2%) 0 0
11 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
12 1 1 (1.2%) 1 (1.2%) 0
13 2 0 2 (2.4%) 0
14 4 1 (1.2%) 0 0
15 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
16 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
17 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
18 2 0 2 (2.4%) 0
19 DIARRHOEA - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
20 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
21 2 0 2 (2.4%) 0
22 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> <NA> <NA>
23 - Overall - - Any Grade - 8 (9.3%) 25 (29.8%) 24 (28.6%)
24 1 7 (8.1%) 12 (14.3%) 12 (14.3%)
25 2 0 4 (4.8%) 4 (4.8%)
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 Grade 1-2 22 (25.6%) 32 (38.1%) 30 (35.7%)
3 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
4 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
5 Grade 3-4 4 (4.7%) 10 (11.9%) 10 (11.9%)
6 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
7 4 1 (1.2%) 0 2 (2.4%)
8 CARDIAC DISORDERS <NA> <NA> <NA>
9 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
10 Grade 1-2 1 (1.2%) 3 (3.6%) 0
11 1 1 (1.2%) 1 (1.2%) 0
12 2 0 2 (2.4%) 0
13 Grade 3-4 1 (1.2%) 0 0
14 4 1 (1.2%) 0 0
15 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
16 Grade 1-2 1 (1.2%) 3 (3.6%) 0
17 1 1 (1.2%) 1 (1.2%) 0
18 2 0 2 (2.4%) 0
19 Grade 3-4 1 (1.2%) 0 0
20 4 1 (1.2%) 0 0
21 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
22 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
23 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
24 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
25 2 0 2 (2.4%) 0
Code
as.data.frame(tbl)[1, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26,0/86, 30.233% 42,0/84, 50.000% 40,0/84, 47.619%
tbl_hierarchical_rate_by_grade(include_overall) works
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 - Any adverse events - - Any Grade - 26 (30.2%) 42 (50.0%) 40 (47.6%)
2 Grade 1-2 22 (25.6%) 32 (38.1%) 30 (35.7%)
3 1 20 (23.3%) 23 (27.4%) 20 (23.8%)
4 2 2 (2.3%) 9 (10.7%) 10 (11.9%)
5 Grade 3-4 4 (4.7%) 10 (11.9%) 10 (11.9%)
6 3 3 (3.5%) 10 (11.9%) 8 (9.5%)
7 4 1 (1.2%) 0 2 (2.4%)
8 CARDIAC DISORDERS <NA> <NA> <NA>
9 - Overall - - Any Grade - 2 (2.3%) 3 (3.6%) 0
10 Grade 1-2 1 (1.2%) 3 (3.6%) 0
11 1 1 (1.2%) 1 (1.2%) 0
12 2 0 2 (2.4%) 0
13 Grade 3-4 1 (1.2%) 0 0
14 4 1 (1.2%) 0 0
15 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
16 Grade 1-2 1 (1.2%) 3 (3.6%) 0
17 1 1 (1.2%) 1 (1.2%) 0
18 2 0 2 (2.4%) 0
19 Grade 3-4 1 (1.2%) 0 0
20 4 1 (1.2%) 0 0
21 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
22 - Overall - - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
23 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
24 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
25 2 0 2 (2.4%) 0
Code
as.data.frame(tbl)[1:25, ]
Output
MedDRA System Organ Class \n MedDRA Preferred Term Grade Placebo \n(N = 86) Xanomeline High Dose \n(N = 84) Xanomeline Low Dose \n(N = 84)
1 CARDIAC DISORDERS <NA> <NA> <NA>
2 ATRIOVENTRICULAR BLOCK SECOND DEGREE - Any Grade - 2 (2.3%) 3 (3.6%) 0
3 Grade 1-2 1 (1.2%) 3 (3.6%) 0
4 1 1 (1.2%) 1 (1.2%) 0
5 2 0 2 (2.4%) 0
6 Grade 3-4 1 (1.2%) 0 0
7 4 1 (1.2%) 0 0
8 GASTROINTESTINAL DISORDERS <NA> <NA> <NA>
9 DIARRHOEA - Any Grade - 9 (10.5%) 4 (4.8%) 5 (6.0%)
10 Grade 1-2 9 (10.5%) 4 (4.8%) 5 (6.0%)
11 1 9 (10.5%) 2 (2.4%) 5 (6.0%)
12 2 0 2 (2.4%) 0
13 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS <NA> <NA> <NA>
14 APPLICATION SITE ERYTHEMA - Any Grade - 3 (3.5%) 15 (17.9%) 12 (14.3%)
15 Grade 1-2 3 (3.5%) 12 (14.3%) 7 (8.3%)
16 1 3 (3.5%) 9 (10.7%) 4 (4.8%)
17 2 0 3 (3.6%) 3 (3.6%)
18 Grade 3-4 0 3 (3.6%) 5 (6.0%)
19 3 0 3 (3.6%) 3 (3.6%)
20 4 0 0 2 (2.4%)
21 APPLICATION SITE PRURITUS - Any Grade - 6 (7.0%) 22 (26.2%) 22 (26.2%)
22 Grade 1-2 5 (5.8%) 15 (17.9%) 17 (20.2%)
23 1 5 (5.8%) 10 (11.9%) 13 (15.5%)
24 2 0 5 (6.0%) 4 (4.8%)
25 Grade 3-4 1 (1.2%) 7 (8.3%) 5 (6.0%)
tbl_hierarchical_rate_by_grade() error messaging works
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grades_exclude = 4:5)
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! The `grades_exclude` argument must be class <character> or empty, not an integer vector.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grade_groups = list("Grade 5" ~ "5"))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade groups must be specified via a named list where each list element is a character vector of the grades to include in the grade group and each name is the corresponding name of the grade group. For example, `"Grade 3-4" = c("3", "4")`.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grade_groups = list(`Grade 3-4` = c("3", "4"), `Grade 4-5` = c("4", "5")))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade groups specified via `grade_groups` cannot overlap. Please ensure that each grade is included in at most one grade group.
Code
tbl <- tbl_hierarchical_rate_by_grade(ADAE_subset, variables = c(AEBODSYS,
AEDECOD, AETOXGR), denominator = ADSL, by = TRTA, label = label,
grades_exclude = as.character(c(1:3, 5:7)))
Condition
Error in `tbl_hierarchical_rate_by_grade()`:
! Grade(s) "6" and "7" supplied to `grades_exclude` are invalid. All grades specified via `grades_exclude` must be levels of "AETOXGR".
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