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   A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  FMQ (Narrow)                (N=134)      (N=134)        (N=132)                 (N=268)           
————————————————————————————————————————————————————————————————————————————————————————————————————
cl A.1                                                                                              
  FMQ1                       17 (12.7%)   14 (10.4%)     29 (22.0%)          -2.2 (-9.9 - 5.4)      
  FMQ2                       23 (17.2%)   20 (14.9%)     20 (15.2%)          -2.2 (-11.0 - 6.5)     
  FMQ3                       20 (14.9%)   19 (14.2%)     23 (17.4%)          -0.7 (-9.2 - 7.7)      
cl B.1                                                                                              
  FMQ1                        8 (6.0%)    11 (8.2%)       7 (5.3%)            2.2 (-3.9 - 8.4)      
  FMQ2                        5 (3.7%)    12 (9.0%)      16 (12.1%)          5.2 (-0.6 - 11.0)      
  FMQ3                       10 (7.5%)     7 (5.2%)       5 (3.8%)           -2.2 (-8.1 - 3.6)      
cl B.2                                                                                              
  FMQ1                       13 (9.7%)    15 (11.2%)      9 (6.8%)            1.5 (-5.8 - 8.8)      
  FMQ2                       12 (9.0%)     9 (6.7%)      10 (7.6%)           -2.2 (-8.7 - 4.2)      
  FMQ3                        6 (4.5%)     7 (5.2%)       9 (6.8%)            0.7 (-4.4 - 5.9)      
cl C.2                                                                                              
  FMQ1                        9 (6.7%)     9 (6.7%)      12 (9.1%)            0.0 (-6.0 - 6.0)      
  FMQ2                        6 (4.5%)     8 (6.0%)       8 (6.1%)            1.5 (-3.8 - 6.8)      
  FMQ3                        6 (4.5%)     9 (6.7%)      10 (7.6%)            2.2 (-3.3 - 7.7)      
cl D.1                                                                                              
  FMQ1                       23 (17.2%)   17 (12.7%)     27 (20.5%)          -4.5 (-13.0 - 4.0)     
  FMQ2                       22 (16.4%)   20 (14.9%)     25 (18.9%)          -1.5 (-10.2 - 7.2)     
  FMQ3                       15 (11.2%)   19 (14.2%)     21 (15.9%)          3.0 (-5.0 - 10.9)      
cl D.2                                                                                              
  FMQ1                        8 (6.0%)    11 (8.2%)       9 (6.8%)            2.2 (-3.9 - 8.4)      
  FMQ2                       14 (10.4%)   15 (11.2%)     14 (10.6%)           0.7 (-6.7 - 8.2)      
  FMQ3                       11 (8.2%)     9 (6.7%)      11 (8.3%)           -1.5 (-7.8 - 4.8)      
# 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
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_10(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

make_table_10()

Required variables:

  • adae: USUBJID, AEBODSYS, AESER, and the variables specified by arm_var, saffl_var, fmqsc_var, and fmqnam_var.
  • alt_counts_df (if specified): USUBJID and the variables specified by arm_var and saffl_var.
Argument Description Default
adae (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
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.