Tabulate Adverse Events by Grade (max, ≥x, ==x)

This function creates summary tables of adverse events (AEs) by grade, for each treatment arm if provided. By default, it shows three measures:

• "max": highest AE grade experienced by each patient

• "sup": at least one AE of grade ≥ x

• "eq": at least one AE of grade == x

Converts an object of class ae_table_grade to a formatted flextable.

Usage

ae_table_grade(
  data_ae,
  ...,
  data_pat,
  measure = c("max", "sup", "eq"),
  arm = NULL,
  grade = "AEGR",
  subjid = "SUBJID",
  ae_label = "AE",
  percent_pattern = "{n} ({p}%)",
  percent_digits = 0,
  zero_value = "0",
  total = TRUE,
  na_strategy = list(display = "always", grouped = TRUE)
)

# S3 method for class 'ae_table_grade'
as_flextable(x, ..., padding_v = NULL)

Arguments

data_ae

Data frame of adverse events, with one row per AE.

...

Unused.

data_pat

Data frame of enrolled patients, with one row per patient.

measure

Character vector specifying which variants to compute: "max", "sup", "eq".

arm

Name of the arm column in data_pat. If NULL, all patients are pooled.

grade

Name of the AE grade column in data_ae.

subjid

Name of the subject ID column (in both data frames).

ae_label

Label used in the output tables (e.g. "AE", "Toxicity").

percent_pattern

Pattern used to format counts and percentages. Use {n} and {p} as placeholders.

percent_digits

Number of digits to show for percentages.

zero_value

String to use when count is zero.

total

Logical. If TRUE, adds a "Total" column across arms (only if multiple arms exist).

na_strategy

A named list controlling how missing AEs or absent patients are displayed in the output tables. Must contain display (one of "if_any" or "always") and grouped (logical).

x

An object of class ae_table_grade.

padding_v

Vertical padding for cells.

Value

A data frame of class ae_table_grade, ready for use with as_flextable().

A flextable object ready to print or export.

Examples

db = grstat_example(N=200, p_na=0.1)
ae_table_grade(db$ae, data_pat=db$enrolres,
               total=FALSE, percent_digits=1) %>%
  as_flextable()
Measure
Level
All patients
(N=200)
Patients by maximum AE grade
Grade 1
41 (20.5%)
Grade 2
64 (32.0%)
Grade 3
50 (25.0%)
Grade 4
31 (15.5%)
Grade 5
3 (1.5%)
Patients with at least one AE at or above each grade
Grade ≥ 1
189 (94.5%)
Grade ≥ 2
148 (74.0%)
Grade ≥ 3
84 (42.0%)
Grade ≥ 4
34 (17.0%)
Grade = 5
3 (1.5%)
Patients with at least one AE at each grade
Grade 1
156 (78.0%)
Grade 2
103 (51.5%)
Grade 3
56 (28.0%)
Grade 4
33 (16.5%)
Grade 5
3 (1.5%)
AE grade completeness
No AE reported
8 (4.0%)
All grades missing
3 (1.5%)
Some grades missing
59 (29.5%)

db = grstat_example(N=20, p_na=0)
ae_table_grade(db$ae, data_pat=db$enrolres, arm="ARM",
               measure=c("max", "sup"),
               total=TRUE, zero_value="-",
               na_strategy=list(display="always", grouped=TRUE)) %>%
  as_flextable()
Measure
Level
Treatment arm
Total
Control
(N=10)
Treatment
(N=10)
Patients by maximum AE grade
Grade 1
4 (40%)
4 (40%)
8 (40%)
Grade 2
2 (20%)
1 (10%)
3 (15%)
Grade 3
3 (30%)
-
3 (15%)
Grade 4
1 (10%)
4 (40%)
5 (25%)
Grade 5
-
1 (10%)
1 (5%)
Patients with at least one AE at or above each grade
Grade ≥ 1
10 (100%)
10 (100%)
20 (100%)
Grade ≥ 2
6 (60%)
6 (60%)
12 (60%)
Grade ≥ 3
4 (40%)
5 (50%)
9 (45%)
Grade ≥ 4
1 (10%)
5 (50%)
6 (30%)
Grade = 5
-
1 (10%)
1 (5%)
AE grade completeness
No AE reported
-
-
-
All grades missing
-
-
-
Some grades missing
-
-
-