FDA Table 12

Patients With Adverse Events Leading to Treatment Discontinuation by System Organ Class and Preferred Term, Safety Population, Pooled Analyses

Body System or Organ Class                                 A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  Dictionary-Derived Term                                   (N=134)      (N=134)        (N=132)                 (N=268)           
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Patients with at least one AE leading to discontinuation   86 (64.2%)   93 (69.4%)     90 (68.2%)          5.2 (-6.0 - 16.5)      
cl A.1                                                     53 (39.6%)   55 (41.0%)     69 (52.3%)          1.5 (-10.3 - 13.2)     
  dcd A.1.1.1.1                                            37 (27.6%)   37 (27.6%)     50 (37.9%)          0.0 (-10.7 - 10.7)     
  dcd A.1.1.1.2                                            33 (24.6%)   31 (23.1%)     40 (30.3%)          -1.5 (-11.7 - 8.7)     
cl B.1                                                     35 (26.1%)   41 (30.6%)     36 (27.3%)          4.5 (-6.3 - 15.3)      
  dcd B.1.1.1.1                                            35 (26.1%)   41 (30.6%)     36 (27.3%)          4.5 (-6.3 - 15.3)      
cl B.2                                                     55 (41.0%)   56 (41.8%)     65 (49.2%)          0.7 (-11.0 - 12.5)     
  dcd B.2.1.2.1                                            36 (26.9%)   33 (24.6%)     35 (26.5%)          -2.2 (-12.7 - 8.2)     
  dcd B.2.2.3.1                                            34 (25.4%)   41 (30.6%)     41 (31.1%)          5.2 (-5.5 - 16.0)      
cl C.1                                                     28 (20.9%)   36 (26.9%)     32 (24.2%)          6.0 (-4.2 - 16.2)      
  dcd C.1.1.1.3                                            28 (20.9%)   36 (26.9%)     32 (24.2%)          6.0 (-4.2 - 16.2)      
cl C.2                                                     26 (19.4%)   39 (29.1%)     43 (32.6%)          9.7 (-0.5 - 19.9)      
  dcd C.2.1.2.1                                            26 (19.4%)   39 (29.1%)     43 (32.6%)          9.7 (-0.5 - 19.9)      
cl D.1                                                     51 (38.1%)   51 (38.1%)     60 (45.5%)          0.0 (-11.6 - 11.6)     
  dcd D.1.1.1.1                                            29 (21.6%)   31 (23.1%)     37 (28.0%)          1.5 (-8.5 - 11.5)      
  dcd D.1.1.4.2                                            33 (24.6%)   34 (25.4%)     39 (29.5%)          0.7 (-9.6 - 11.1)      
cl D.2                                                     35 (26.1%)   46 (34.3%)     44 (33.3%)          8.2 (-2.7 - 19.2)      
  dcd D.2.1.5.3                                            35 (26.1%)   46 (34.3%)     44 (33.3%)          8.2 (-2.7 - 19.2)      
# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variable DCSREAS exist in adae
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"

# Select Preferred Term Variable
pref_var <- "AEDECOD"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_12(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff)

make_table_12()

Required variables:

  • adae: USUBJID, AEBODSYS, DCSREAS, and the variables specified by pref_var, arm_var, and saffl_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"
pref_var (character) Preferred term variable from adae to include in the table. "AEDECOD"
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
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.