FDA Table 18

Patients With Adverse Events by Female-Specific FDA Medical Query (Broad) and Preferred Term, Female Safety Population, Pooled Analyses

FMQ (Broad)                    A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  Preferred Term                (N=134)      (N=134)        (N=132)                 (N=268)           
——————————————————————————————————————————————————————————————————————————————————————————————————————
Abnormal Uterine Bleeding                                                                             
  dcd B.2.2.3.1                 6 (4.5%)    14 (10.4%)      6 (4.5%)           6.0 (-0.3 - 12.2)      
  dcd C.1.1.1.3                14 (10.4%)   13 (9.7%)      10 (7.6%)           -0.7 (-8.0 - 6.5)      
Amenorrhea                                                                                            
  dcd B.2.2.3.1                12 (9.0%)    10 (7.5%)      10 (7.6%)           -1.5 (-8.1 - 5.1)      
  dcd C.1.1.1.3                13 (9.7%)    11 (8.2%)      10 (7.6%)           -1.5 (-8.3 - 5.3)      
Bacterial Vaginosis                                                                                   
  dcd B.2.2.3.1                10 (7.5%)    10 (7.5%)       8 (6.1%)            0.0 (-6.3 - 6.3)      
  dcd C.1.1.1.3                 8 (6.0%)    13 (9.7%)       5 (3.8%)           3.7 (-2.7 - 10.2)      
Decreased Menstrual Bleeding                                                                          
  dcd B.2.2.3.1                10 (7.5%)     5 (3.7%)       9 (6.8%)           -3.7 (-9.2 - 1.8)      
  dcd C.1.1.1.3                 3 (2.2%)    10 (7.5%)      12 (9.1%)            5.2 (0.1 - 10.3)      
# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variables FMQ01SC and FMQ01NAM exist in adae
set.seed(1)
adae <- dplyr::rename(adae, FMQ01SC = SMQ01SC, FMQ01NAM = SMQ01NAM)
levels(adae$FMQ01SC) <- c("BROAD", "NARROW")
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"
adae$FMQ01NAM <- factor(adae$FMQ01NAM, levels = c(
  unique(adae$FMQ01NAM), "Abnormal Uterine Bleeding", "Amenorrhea",
  "Bacterial Vaginosis", "Decreased Menstrual Bleeding"
))
adae$FMQ01NAM[adae$SEX == "F"] <- as.factor(
  sample(c(
    "Abnormal Uterine Bleeding", "Amenorrhea",
    "Bacterial Vaginosis", "Decreased Menstrual Bleeding"
  ), sum(adae$SEX == "F"), replace = TRUE)
)

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X")
make_table_18(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

make_table_18()

Required variables:

  • adae: adae must contain USUBJID, SEX, and the variables specified by arm_var, saffl_var, pref_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"
pref_var (character) Preferred term variable to use in table. "AEDECOD"
sex_scope (character) Level of SEX to output in table. "F"
fmq_scope (character) FMQ scope value to use in table. "BROAD"
fmqsc_var (character) FMQ scope variable to use in table. "FMQ01SC"
fmqnam_var (character) FMQ reference name variable to use in table. "FMQ01NAM"
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.