FDA Table 13

Patients With Common Adverse Events Occurring at >=X% Frequency, Safety Population, Pooled Analyses

                          A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
Dictionary-Derived Term    (N=134)      (N=134)        (N=132)                 (N=268)           
—————————————————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1             50 (37.3%)   45 (33.6%)     63 (47.7%)          -3.7 (-15.2 - 7.7)     
dcd B.2.2.3.1             48 (35.8%)   54 (40.3%)     51 (38.6%)          4.5 (-7.1 - 16.1)      
dcd C.2.1.2.1             35 (26.1%)   48 (35.8%)     55 (41.7%)          9.7 (-1.3 - 20.7)      
dcd D.2.1.5.3             47 (35.1%)   58 (43.3%)     57 (43.2%)          8.2 (-3.4 - 19.9)      
# Load Libraries & Data
library(cardinal)

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

# Select Preferred Term Variable
pref_var <- "AEDECOD"

# Select Minimum Frequency (%)
min_freq <- 0.40

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_13(adae = adae, alt_counts_df = adsl, pref_var = pref_var, min_freq = min_freq, risk_diff = risk_diff)

make_table_13()

Required variables:

  • adae: USUBJID 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 (typically ADSL) used only to calculate column counts. NULL
show_colcounts (flag) Whether column counts should be printed. TRUE
min_freq (proportion) Minimum % frequency (fraction of N) required in any column to include each row. 0.05
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_pref_var (character) Label corresponding to preferred term variable pref_var to print in the table. formatters::var_labels(adae, fill = TRUE)[pref_var]
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
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.