FDA Table 35

Patients With Adverse Events by System Organ Class, Safety Population, Pooled Analysis (or Trial X)

gtsummary Table Setup 
# Load Libraries & Data
library(cardinal)

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

# Output Table
make_table_35(df = adae, denominator = adsl, return_ard = FALSE)
Function Details

make_table_35()

Required variables:

  • df: The variables specified by id_var, arm_var, saffl_var, and soc_var.
  • denominator (if specified): USUBJID and the variables specified by arm_var and saffl_var
  • If both the ARD (return_ard = TRUE) and an overall column (lbl_overall not missing) are requested, a list of two ARDs will be returned: one for the table by groups, and the other for the overall column.
Argument Description Default
df (data.frame) Dataset (typically ADSL) required to build table. No default
return_ard (flag) Whether an ARD should be returned. TRUE
denominator (character) Alternative dataset used only to calculate column counts. NULL
id_var (character) Identifier variable used to count the participants within each flag. "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"
soc_var (character) SOC variable from adae to include in the table. "ARBODSYS"
na_level (character) String to represent missing values. "<Missing>"
lbl_overall (character) String to represent the label of an overall column. NULL

Source code for this function is available here.

ARD Setup 
# Load Libraries & Data
library(cardinal)

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

# Create Table and ARD
result <- make_table_35(df = adae, denominator = adsl)

# Output ARD
result$ard
$tbl_hierarchical
{cards} data frame: 72 x 13
   group1 group1_level variable variable_level   context stat_name stat_label  stat stat_fmt fmt_fn warning error gts_column
1     ARM    A: Drug X AEBODSYS         cl A.1 hierarch…         n          n    78       78   <fn>                   stat_1
2     ARM    A: Drug X AEBODSYS         cl A.1 hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X AEBODSYS         cl A.1 hierarch…         p          % 0.582       58   <fn>                   stat_1
4     ARM    A: Drug X AEBODSYS         cl B.1 hierarch…         n          n    47       47   <fn>                   stat_1
5     ARM    A: Drug X AEBODSYS         cl B.1 hierarch…         N          N   134      134   <fn>                   stat_1
6     ARM    A: Drug X AEBODSYS         cl B.1 hierarch…         p          % 0.351       35   <fn>                   stat_1
7     ARM    A: Drug X AEBODSYS         cl B.2 hierarch…         n          n    79       79   <fn>                   stat_1
8     ARM    A: Drug X AEBODSYS         cl B.2 hierarch…         N          N   134      134   <fn>                   stat_1
9     ARM    A: Drug X AEBODSYS         cl B.2 hierarch…         p          %  0.59       59   <fn>                   stat_1
10    ARM    A: Drug X AEBODSYS         cl C.1 hierarch…         n          n    43       43   <fn>                   stat_1
ℹ 62 more rows
ℹ Use `print(n = ...)` to see more rows
rtables Table Setup 
# Load Libraries & Data
library(random.cdisc.data)
library(cardinal)

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

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_35_rtables(df = adae, alt_counts_df = adsl, risk_diff = risk_diff)
                             A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
Body System or Organ Class    (N=134)      (N=134)        (N=132)                 (N=268)           
————————————————————————————————————————————————————————————————————————————————————————————————————
cl A.1                       78 (58.2%)   75 (56.0%)     89 (67.4%)          -2.2 (-14.1 - 9.6)     
cl B.2                       79 (59.0%)   74 (55.2%)     85 (64.4%)          -3.7 (-15.6 - 8.1)     
cl D.1                       79 (59.0%)   67 (50.0%)     80 (60.6%)          -9.0 (-20.8 - 2.9)     
cl D.2                       47 (35.1%)   58 (43.3%)     57 (43.2%)          8.2 (-3.4 - 19.9)      
cl B.1                       47 (35.1%)   49 (36.6%)     43 (32.6%)          1.5 (-10.0 - 13.0)     
cl C.2                       35 (26.1%)   48 (35.8%)     55 (41.7%)          9.7 (-1.3 - 20.7)      
cl C.1                       43 (32.1%)   46 (34.3%)     43 (32.6%)          2.2 (-9.0 - 13.5)
Function Details

make_table_35_rtables()

Required variables:

  • df: USUBJID and the variables specified by arm_var, saffl_var and soc_var.
  • alt_counts_df (if specified): USUBJID and the variables specified by 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 (typically ADSL) used only to calculate column counts. NULL
show_colcounts (flag) Whether column counts should be printed. TRUE
id_var (character) Subject identifier 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"
soc_var (character) SOC variable from adae to include in the table. "AEDECOD"
lbl_soc_var (character) Label corresponding to SOC variable soc_var to print in the table. formatters::var_labels(adae, fill = TRUE)[soc_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
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.