FDA Table 10

Patients With Serious Adverse Events by System Organ Class and FDA Medical Query (Narrow), Safety Population, Pooled Analyses

Body System or Organ Class
    FMQ (Narrow) 		A: Drug X
N = 1341 		B: Placebo
N = 1341 		C: Combination
N = 1321
cl A.1


    FMQ1 17 (13%) 14 (10%) 29 (22%)
    FMQ2 23 (17%) 20 (15%) 20 (15%)
    FMQ3 20 (15%) 19 (14%) 23 (17%)
cl B.1


    FMQ1 8 (6.0%) 11 (8.2%) 7 (5.3%)
    FMQ2 5 (3.7%) 12 (9.0%) 16 (12%)
    FMQ3 10 (7.5%) 7 (5.2%) 5 (3.8%)
cl B.2


    FMQ1 13 (9.7%) 15 (11%) 9 (6.8%)
    FMQ2 12 (9.0%) 9 (6.7%) 10 (7.6%)
    FMQ3 6 (4.5%) 7 (5.2%) 9 (6.8%)
cl C.2


    FMQ1 9 (6.7%) 9 (6.7%) 12 (9.1%)
    FMQ2 6 (4.5%) 8 (6.0%) 8 (6.1%)
    FMQ3 6 (4.5%) 9 (6.7%) 10 (7.6%)
cl D.1


    FMQ1 23 (17%) 17 (13%) 27 (20%)
    FMQ2 22 (16%) 20 (15%) 25 (19%)
    FMQ3 15 (11%) 19 (14%) 21 (16%)
cl D.2


    FMQ1 8 (6.0%) 11 (8.2%) 9 (6.8%)
    FMQ2 14 (10%) 15 (11%) 14 (11%)
    FMQ3 11 (8.2%) 9 (6.7%) 11 (8.3%)
1 n (%) 
# Load Libraries & Data
library(dplyr)
library(cards)
library(cardinal)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae %>%
  rename(FMQ01SC = SMQ01SC) %>%
  mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
make_table_10(df = adae, denominator = adsl, return_ard = FALSE)

make_table_10()

Required variables:

  • df: AEBODSYS, AESER, and the variables specified by id_var, arm_var, saffl_var, fmqsc_var, and fmqnam_var.
  • denominator (if specified): The variables specified by id_var, arm_var and saffl_var.
Argument Description Default
df (data.frame) Dataset (typically ADAE) required to build table. No default
denominator (character) Alternative dataset used only to calculate column counts. NULL
return_ard (flag) Whether column counts should be printed. TRUE
id_var (character) Name of the unique subject identifiers variable. "USUBJID"
arm_var (character) Arm variable used to split table into columns. "ARM"
saffl_var (character) Flag variable used to indicate inclusion in safety population. "SAFFL"
fmqsc_var (character) FMQ scope variable to use in table. "FMQ01SC"
fmqnam_var (character) FMQ reference name variable to use in table. "FMQ01NAM"
fmq_scope (character) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’. "NARROW"
na_level (character) String to represent missing values. "<Missing>"

Source code for this function is available here.

group1 group1_level group2 group2_level variable variable_level context stat_name stat_label stat fmt_fn warning error
ARM 1 AEBODSYS 1 FMQ01NAM 1 hierarchical n n 17 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 1 hierarchical p % 0.1268657 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 2 hierarchical n n 23 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 2 hierarchical p % 0.1716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 3 hierarchical n n 20 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 1 FMQ01NAM 3 hierarchical p % 0.1492537 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 1 hierarchical n n 8 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 1 hierarchical p % 0.05970149 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 2 hierarchical n n 5 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 2 hierarchical p % 0.03731343 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 3 hierarchical n n 10 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 2 FMQ01NAM 3 hierarchical p % 0.07462687 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 1 hierarchical n n 13 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 1 hierarchical p % 0.09701493 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 2 hierarchical n n 12 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 2 hierarchical p % 0.08955224 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 3 hierarchical n n 6 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 3 FMQ01NAM 3 hierarchical p % 0.04477612 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 1 hierarchical n n 9 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 1 hierarchical p % 0.06716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 2 hierarchical n n 6 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 2 hierarchical p % 0.04477612 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 3 hierarchical n n 6 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 5 FMQ01NAM 3 hierarchical p % 0.04477612 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 1 hierarchical n n 23 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 1 hierarchical p % 0.1716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 2 hierarchical n n 22 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 2 hierarchical p % 0.1641791 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 3 hierarchical n n 15 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 6 FMQ01NAM 3 hierarchical p % 0.1119403 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 1 hierarchical n n 8 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 1 hierarchical p % 0.05970149 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 2 hierarchical n n 14 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 2 hierarchical p % 0.1044776 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 3 hierarchical n n 11 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 1 AEBODSYS 7 FMQ01NAM 3 hierarchical p % 0.08208955 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 1 hierarchical n n 14 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 1 hierarchical p % 0.1044776 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 2 hierarchical n n 20 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 2 hierarchical p % 0.1492537 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 3 hierarchical n n 19 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 1 FMQ01NAM 3 hierarchical p % 0.141791 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 1 hierarchical n n 11 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 1 hierarchical p % 0.08208955 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 2 hierarchical n n 12 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 2 hierarchical p % 0.08955224 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 3 hierarchical n n 7 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 2 FMQ01NAM 3 hierarchical p % 0.05223881 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 1 hierarchical n n 15 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 1 hierarchical p % 0.1119403 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 2 hierarchical n n 9 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 2 hierarchical p % 0.06716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 3 hierarchical n n 7 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 3 FMQ01NAM 3 hierarchical p % 0.05223881 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 1 hierarchical n n 9 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 1 hierarchical p % 0.06716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 2 hierarchical n n 8 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 2 hierarchical p % 0.05970149 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 3 hierarchical n n 9 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 5 FMQ01NAM 3 hierarchical p % 0.06716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 1 hierarchical n n 17 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 1 hierarchical p % 0.1268657 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 2 hierarchical n n 20 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 2 hierarchical p % 0.1492537 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 3 hierarchical n n 19 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 6 FMQ01NAM 3 hierarchical p % 0.141791 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 1 hierarchical n n 11 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 1 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 1 hierarchical p % 0.08208955 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 2 hierarchical n n 15 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 2 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 2 hierarchical p % 0.1119403 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 3 hierarchical n n 9 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 3 hierarchical N N 134 0 NULL NULL
ARM 2 AEBODSYS 7 FMQ01NAM 3 hierarchical p % 0.06716418 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 1 hierarchical n n 29 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 1 hierarchical p % 0.219697 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 2 hierarchical n n 20 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 2 hierarchical p % 0.1515152 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 3 hierarchical n n 23 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 1 FMQ01NAM 3 hierarchical p % 0.1742424 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 1 hierarchical n n 7 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 1 hierarchical p % 0.0530303 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 2 hierarchical n n 16 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 2 hierarchical p % 0.1212121 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 3 hierarchical n n 5 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 2 FMQ01NAM 3 hierarchical p % 0.03787879 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 1 hierarchical n n 9 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 1 hierarchical p % 0.06818182 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 2 hierarchical n n 10 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 2 hierarchical p % 0.07575758 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 3 hierarchical n n 9 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 3 FMQ01NAM 3 hierarchical p % 0.06818182 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 1 hierarchical n n 12 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 1 hierarchical p % 0.09090909 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 2 hierarchical n n 8 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 2 hierarchical p % 0.06060606 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 3 hierarchical n n 10 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 5 FMQ01NAM 3 hierarchical p % 0.07575758 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 1 hierarchical n n 27 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 1 hierarchical p % 0.2045455 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 2 hierarchical n n 25 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 2 hierarchical p % 0.1893939 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 3 hierarchical n n 21 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 6 FMQ01NAM 3 hierarchical p % 0.1590909 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 1 hierarchical n n 9 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 1 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 1 hierarchical p % 0.06818182 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 2 hierarchical n n 14 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 2 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 2 hierarchical p % 0.1060606 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 3 hierarchical n n 11 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 3 hierarchical N N 132 0 NULL NULL
ARM 3 AEBODSYS 7 FMQ01NAM 3 hierarchical p % 0.08333333 function (x) , {, res <- ifelse(is.na(x), NA_character_, str_trim(format(round_fun(x * , scale, digits = digits), nsmall = digits))), if (!is.null(width)) {, res <- ifelse(nchar(res) >= width | is.na(res), res, , paste0(strrep(” “, width - nchar(res)), res)), }, res, } NULL NULL 
# Load Libraries & Data
library(dplyr)
library(cards)
library(cardinal)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae %>%
  rename(FMQ01SC = SMQ01SC) %>%
  mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output ARD
output <- make_table_10(df = adae, denominator = adsl)
output$ard
Body System or Organ Class   A: Drug X    B: Placebo   C: Combination
  FMQ (Narrow)                (N=134)      (N=134)        (N=132)    
—————————————————————————————————————————————————————————————————————
cl A.1                                                               
  FMQ1                       17 (12.7%)   14 (10.4%)     29 (22.0%)  
  FMQ2                       23 (17.2%)   20 (14.9%)     20 (15.2%)  
  FMQ3                       20 (14.9%)   19 (14.2%)     23 (17.4%)  
cl B.1                                                               
  FMQ1                        8 (6.0%)    11 (8.2%)       7 (5.3%)   
  FMQ2                        5 (3.7%)    12 (9.0%)      16 (12.1%)  
  FMQ3                       10 (7.5%)     7 (5.2%)       5 (3.8%)   
cl B.2                                                               
  FMQ1                       13 (9.7%)    15 (11.2%)      9 (6.8%)   
  FMQ2                       12 (9.0%)     9 (6.7%)      10 (7.6%)   
  FMQ3                        6 (4.5%)     7 (5.2%)       9 (6.8%)   
cl C.2                                                               
  FMQ1                        9 (6.7%)     9 (6.7%)      12 (9.1%)   
  FMQ2                        6 (4.5%)     8 (6.0%)       8 (6.1%)   
  FMQ3                        6 (4.5%)     9 (6.7%)      10 (7.6%)   
cl D.1                                                               
  FMQ1                       23 (17.2%)   17 (12.7%)     27 (20.5%)  
  FMQ2                       22 (16.4%)   20 (14.9%)     25 (18.9%)  
  FMQ3                       15 (11.2%)   19 (14.2%)     21 (15.9%)  
cl D.2                                                               
  FMQ1                        8 (6.0%)    11 (8.2%)       9 (6.8%)   
  FMQ2                       14 (10.4%)   15 (11.2%)     14 (10.6%)  
  FMQ3                       11 (8.2%)     9 (6.7%)      11 (8.3%)   
# Load Libraries & Data
# library(dplyr)
library(cardinal)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae %>%
  rename(FMQ01SC = SMQ01SC) %>%
  mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
make_table_10_rtables(df = adae, alt_counts_df = adsl)

make_table_10_rtables()

Required variables:

  • df: AEBODSYS, AESER, and the variables specified by id_var, arm_var, saffl_var, fmqsc_var, and fmqnam_var.
  • alt_counts_df (if specified): The variables specified by id_var, arm_var and saffl_var.
Argument Description Default
df (data.frame) Dataset (typically ADAE) required to build table. No default
alt_counts_df (character) Alternative dataset used only to calculate column counts. NULL
show_colcounts (flag) Whether column counts should be printed. TRUE
id_var (character) Name of the unique subject identifiers variable. "ARM"
arm_var (character) Arm variable used to split table into columns. "ARM"
saffl_var (character) Flag variable used to indicate inclusion in safety population. "SAFFL"
fmqsc_var (character) FMQ scope variable to use in table. "FMQ01SC"
fmqnam_var (character) FMQ reference name variable to use in table. "FMQ01NAM"
fmq_scope (character) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’. "NARROW"
lbl_overall (character) If specified, an overall column will be added to the table with the given value as the column label. NULL
risk_diff

(named list) List of settings to apply to add a risk difference column to the table. See tern::add_riskdiff() for more details. List should contain the following elements:

  • arm_x: (required) the name of reference arm.

  • arm_y: (required) the name of the arm to compare to the reference arm.

  • col_label: (optional) label to use for the risk difference column. Defaults to "Risk Difference (%) (95% CI)".

  • pct: (optional) whether the output should be returned as percentages. Defaults to TRUE.

 NULL
prune_0 (flag) Whether all-zero rows should be removed from the table. FALSE
na_level (character) String to represent missing values. "<Missing>"
annotations (named list of character) List of annotations to add to the table. Valid annotation types are title, subtitles, main_footer, and prov_footer. Each name-value pair should use the annotation type as name and the desired string as value. NULL

Source code for this function is available here.