FDA Table 12

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

gtsummary Table Setup

# 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
make_table_12(df = adae, denominator = adsl, return_ard = FALSE, pref_var = pref_var)

Body System or Organ Class Dictionary-Derived Term	A: Drug X N = 134¹	B: Placebo N = 134¹	C: Combination N = 132¹
Number of patients with event	86 (64%)	93 (69%)	90 (68%)
cl A.1	53 (40%)	55 (41%)	69 (52%)
dcd A.1.1.1.1	37 (28%)	37 (28%)	50 (38%)
dcd A.1.1.1.2	33 (25%)	31 (23%)	40 (30%)
cl B.1	35 (26%)	41 (31%)	36 (27%)
dcd B.1.1.1.1	35 (26%)	41 (31%)	36 (27%)
cl B.2	55 (41%)	56 (42%)	65 (49%)
dcd B.2.1.2.1	36 (27%)	33 (25%)	35 (27%)
dcd B.2.2.3.1	34 (25%)	41 (31%)	41 (31%)
cl C.1	28 (21%)	36 (27%)	32 (24%)
dcd C.1.1.1.3	28 (21%)	36 (27%)	32 (24%)
cl C.2	26 (19%)	39 (29%)	43 (33%)
dcd C.2.1.2.1	26 (19%)	39 (29%)	43 (33%)
cl D.1	51 (38%)	51 (38%)	60 (45%)
dcd D.1.1.1.1	29 (22%)	31 (23%)	37 (28%)
dcd D.1.1.4.2	33 (25%)	34 (25%)	39 (30%)
cl D.2	35 (26%)	46 (34%)	44 (33%)
dcd D.2.1.5.3	35 (26%)	46 (34%)	44 (33%)
¹ n (%)

Function Details

`make_table_12()`

Required variables:

df: 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
`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"`
`pref_var`	(`character`) Name of the preferred term variable from adae to include in the table.	`"AEDECOD"`

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

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

# Select Preferred Term Variable
pref_var <- "AEDECOD"

# Create Table & ARD
result <- make_table_12(df = adae, denominator = adsl, pref_var = pref_var)

# Output ARD
result$ard

{cards} data frame: 90 x 13

   group1 group1_level   group2 group2_level variable variable_level   context stat_name stat_label  stat fmt_fn warning error
1     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    51      0              
2     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
3     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.381   <fn>              
4     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    45      0              
5     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
6     ARM    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.336   <fn>              
7     ARM    A: Drug X AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         n          n    42      0              
8     ARM    A: Drug X AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         N          N   134      0              
9     ARM    A: Drug X AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         p          % 0.313   <fn>              
10    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    48      0              
11    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   134      0              
12    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          % 0.358   <fn>              
13    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    47      0              
14    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   134      0              
15    ARM    A: Drug X AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          % 0.351   <fn>              
16    ARM    A: Drug X AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         n          n    36      0              
17    ARM    A: Drug X AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         N          N   134      0              
18    ARM    A: Drug X AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         p          % 0.269   <fn>              
19    ARM    A: Drug X AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         n          n    35      0              
20    ARM    A: Drug X AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         N          N   134      0              
21    ARM    A: Drug X AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         p          % 0.261   <fn>              
22    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    31      0              
23    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   134      0              
24    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.231   <fn>              
25    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    46      0              
26    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   134      0              
27    ARM    A: Drug X AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.343   <fn>              
28    ARM    A: Drug X AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         n          n    44      0              
29    ARM    A: Drug X AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         N          N   134      0              
30    ARM    A: Drug X AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         p          % 0.328   <fn>              
31    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    52      0              
32    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
33    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.388   <fn>              
34    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    40      0              
35    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
36    ARM    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.299   <fn>              
37    ARM    B: Place… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         n          n    51      0              
38    ARM    B: Place… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         N          N   134      0              
39    ARM    B: Place… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         p          % 0.381   <fn>              
40    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    44      0              
41    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   134      0              
42    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          % 0.328   <fn>              
43    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    57      0              
44    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   134      0              
45    ARM    B: Place… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          % 0.425   <fn>              
46    ARM    B: Place… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         n          n    47      0              
47    ARM    B: Place… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         N          N   134      0              
48    ARM    B: Place… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         p          % 0.351   <fn>              
49    ARM    B: Place… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         n          n    43      0              
50    ARM    B: Place… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         N          N   134      0              
51    ARM    B: Place… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         p          % 0.321   <fn>              
52    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    40      0              
53    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   134      0              
54    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.299   <fn>              
55    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    46      0              
56    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   134      0              
57    ARM    B: Place… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.343   <fn>              
58    ARM    B: Place… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         n          n    58      0              
59    ARM    B: Place… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         N          N   134      0              
60    ARM    B: Place… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         p          % 0.433   <fn>              
61    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    73      0              
62    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
63    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.553   <fn>              
64    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    56      0              
65    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
66    ARM    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.424   <fn>              
67    ARM    C: Combi… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         n          n    52      0              
68    ARM    C: Combi… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         N          N   132      0              
69    ARM    C: Combi… AEBODSYS       cl B.1  AEDECOD      dcd B.1.… hierarch…         p          % 0.394   <fn>              
70    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    44      0              
71    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   132      0              
72    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          % 0.333   <fn>              
73    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         n          n    62      0              
74    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         N          N   132      0              
75    ARM    C: Combi… AEBODSYS       cl B.2  AEDECOD      dcd B.2.… hierarch…         p          %  0.47   <fn>              
76    ARM    C: Combi… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         n          n    53      0              
77    ARM    C: Combi… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         N          N   132      0              
78    ARM    C: Combi… AEBODSYS       cl C.1  AEDECOD      dcd C.1.… hierarch…         p          % 0.402   <fn>              
79    ARM    C: Combi… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         n          n    49      0              
80    ARM    C: Combi… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         N          N   132      0              
81    ARM    C: Combi… AEBODSYS       cl C.2  AEDECOD      dcd C.2.… hierarch…         p          % 0.371   <fn>              
82    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    51      0              
83    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   132      0              
84    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.386   <fn>              
85    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         n          n    52      0              
86    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         N          N   132      0              
87    ARM    C: Combi… AEBODSYS       cl D.1  AEDECOD      dcd D.1.… hierarch…         p          % 0.394   <fn>              
88    ARM    C: Combi… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         n          n    55      0              
89    ARM    C: Combi… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         N          N   132      0              
90    ARM    C: Combi… AEBODSYS       cl D.2  AEDECOD      dcd D.2.… hierarch…         p          % 0.417   <fn>

rtables Table Setup

# 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_rtables(df = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff)

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)

Function Details

`make_table_12_rtables()`

Required variables:

df: 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.