FDA Table 11

Patients with FDA Medical Query (Narrow) Leading to Treatment Discontinuation, Safety Population, Pooled Analyses

Spec. Screenshot

gtsummary Table

gtsummary Table Setup

# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae |>
  dplyr::rename(FMQ01SC = SMQ01SC) |>
  dplyr::mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
make_table_11(df = adae, denominator = adsl, return_ard = FALSE)

Body System or Organ Class     FMQ (Narrow)	A: Drug X N = 1341	B: Placebo N = 1341	C: Combination N = 1321
Number of patients with event	83 (62%)	90 (67%)	88 (67%)
cl A.1	53 (40%)	55 (41%)	69 (52%)
FMQ1	22 (16%)	21 (16%)	37 (28%)
FMQ2	24 (18%)	31 (23%)	33 (25%)
FMQ3	28 (21%)	25 (19%)	31 (23%)
cl B.1	35 (26%)	41 (31%)	36 (27%)
FMQ1	12 (9.0%)	17 (13%)	19 (14%)
FMQ2	9 (6.7%)	21 (16%)	20 (15%)
FMQ3	19 (14%)	11 (8.2%)	7 (5.3%)
cl B.2	36 (27%)	33 (25%)	35 (27%)
FMQ1	16 (12%)	15 (11%)	12 (9.1%)
FMQ2	17 (13%)	12 (9.0%)	16 (12%)
FMQ3	11 (8.2%)	13 (9.7%)	15 (11%)
cl C.2	26 (19%)	39 (29%)	43 (33%)
FMQ1	11 (8.2%)	12 (9.0%)	19 (14%)
FMQ2	11 (8.2%)	15 (11%)	14 (11%)
FMQ3	8 (6.0%)	14 (10%)	14 (11%)
cl D.1	51 (38%)	51 (38%)	60 (45%)
FMQ1	22 (16%)	22 (16%)	32 (24%)
FMQ2	24 (18%)	25 (19%)	33 (25%)
FMQ3	19 (14%)	24 (18%)	26 (20%)
cl D.2	35 (26%)	46 (34%)	44 (33%)
FMQ1	11 (8.2%)	23 (17%)	17 (13%)
FMQ2	18 (13%)	16 (12%)	18 (14%)
FMQ3	11 (8.2%)	16 (12%)	15 (11%)
1 n (%)

Function Details

make_table_11()

---

Required variables:

• df: USUBJID, AEBODSYS, AESER, DCSREAS, and the variables specified by arm_var, saffl_var, fmqsc_var, and fmqnam_var.
• denominator (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"
fmqsc_var	(character) FMQ scope variable to use in table.	"FMQ01SC"
fmqnam_var	(character) FMQ reference name variable to use in table.	"FMQ01NAM"
fmq_scope	(character) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’.	"NARROW"
na_level	(character) String to represent missing values.	"<Missing>"

Source code for this function is available here.

ARD

ARD Setup

# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae |>
  dplyr::rename(FMQ01SC = SMQ01SC) |>
  dplyr::mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Create Table & ARD
result <- make_table_11(df = adae, denominator = adsl)

# Output ARD
result$ard

{cards} data frame: 162 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 FMQ01NAM           FMQ1 hierarch…         n          n    29      0              
2      ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
3      ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.216   <fn>              
4      ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         n          n    28      0              
5      ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
6      ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.209   <fn>              
7      ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         n          n    46      0              
8      ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
9      ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.348   <fn>              
10     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         n          n    13      0              
11     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
12     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.097   <fn>              
13     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         n          n    17      0              
14     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
15     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.127   <fn>              
16     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         n          n    19      0              
17     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
18     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.144   <fn>              
19     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         n          n    19      0              
20     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
21     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.142   <fn>              
22     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         n          n    18      0              
23     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
24     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.134   <fn>              
25     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         n          n    13      0              
26     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
27     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.098   <fn>              
28     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         n          n    14      0              
29     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
30     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.104   <fn>              
31     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         n          n    12      0              
32     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
33     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         p          %  0.09   <fn>              
34     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         n          n    20      0              
35     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
36     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.152   <fn>              
37     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         n          n    26      0              
38     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
39     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.194   <fn>              
40     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         n          n    26      0              
41     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
42     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.194   <fn>              
43     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         n          n    35      0              
44     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
45     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.265   <fn>              
46     ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         n          n    12      0              
47     ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
48     ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         p          %  0.09   <fn>              
49     ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         n          n    24      0              
50     ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         N          N   134      0              
51     ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.179   <fn>              
52     ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         n          n    18      0              
53     ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         N          N   132      0              
54     ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ1 hierarch…         p          % 0.136   <fn>              
55     ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n    31      0              
56     ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
57     ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.231   <fn>              
58     ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n    36      0              
59     ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
60     ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.269   <fn>              
61     ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n    41      0              
62     ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
63     ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.311   <fn>              
64     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         n          n    10      0              
65     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
66     ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.075   <fn>              
67     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         n          n    23      0              
68     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
69     ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.172   <fn>              
70     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         n          n    26      0              
71     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
72     ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.197   <fn>              
73     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         n          n    18      0              
74     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
75     ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.134   <fn>              
76     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         n          n    12      0              
77     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
78     ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         p          %  0.09   <fn>              
79     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         n          n    16      0              
80     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
81     ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.121   <fn>              
82     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         n          n    11      0              
83     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
84     ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.082   <fn>              
85     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         n          n    17      0              
86     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
87     ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.127   <fn>              
88     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         n          n    15      0              
89     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
90     ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.114   <fn>              
91     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         n          n    32      0              
92     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
93     ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.239   <fn>              
94     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         n          n    28      0              
95     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
96     ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.209   <fn>              
97     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         n          n    41      0              
98     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
99     ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.311   <fn>              
100    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         n          n    20      0              
101    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
102    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.149   <fn>              
103    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         n          n    18      0              
104    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         N          N   134      0              
105    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.134   <fn>              
106    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         n          n    19      0              
107    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         N          N   132      0              
108    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ2 hierarch…         p          % 0.144   <fn>              
109    ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         n          n    36      0              
110    ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
111    ARM    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.269   <fn>              
112    ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         n          n    28      0              
113    ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
114    ARM    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.209   <fn>              
115    ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         n          n    42      0              
116    ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
117    ARM    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.318   <fn>              
118    ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         n          n    19      0              
119    ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
120    ARM    A: Drug X AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.142   <fn>              
121    ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         n          n    11      0              
122    ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
123    ARM    B: Place… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.082   <fn>              
124    ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         n          n     7      0              
125    ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
126    ARM    C: Combi… AEBODSYS       cl B.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.053   <fn>              
127    ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         n          n    11      0              
128    ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
129    ARM    A: Drug X AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.082   <fn>              
130    ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         n          n    14      0              
131    ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
132    ARM    B: Place… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.104   <fn>              
133    ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         n          n    15      0              
134    ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
135    ARM    C: Combi… AEBODSYS       cl B.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.114   <fn>              
136    ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         n          n    10      0              
137    ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
138    ARM    A: Drug X AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.075   <fn>              
139    ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         n          n    14      0              
140    ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
141    ARM    B: Place… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.104   <fn>              
142    ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         n          n    14      0              
143    ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
144    ARM    C: Combi… AEBODSYS       cl C.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.106   <fn>              
145    ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         n          n    19      0              
146    ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
147    ARM    A: Drug X AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.142   <fn>              
148    ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         n          n    32      0              
149    ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
150    ARM    B: Place… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.239   <fn>              
151    ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         n          n    27      0              
152    ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
153    ARM    C: Combi… AEBODSYS       cl D.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.205   <fn>              
154    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         n          n    12      0              
155    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
156    ARM    A: Drug X AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         p          %  0.09   <fn>              
157    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         n          n    16      0              
158    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         N          N   134      0              
159    ARM    B: Place… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.119   <fn>              
160    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         n          n    18      0              
161    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         N          N   132      0              
162    ARM    C: Combi… AEBODSYS       cl D.2 FMQ01NAM           FMQ3 hierarch…         p          % 0.136   <fn>              

rtables Table

rtables Table Setup

# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae |>
  dplyr::rename(FMQ01SC = SMQ01SC) |>
  dplyr::mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_11_rtables(df = adae, alt_counts_df = adsl, risk_diff = risk_diff)

Body System or Organ Class                                 A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  FMQ (Narrow)                                              (N=134)      (N=134)        (N=132)                 (N=268)           
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Patients with at least one AE leading to discontinuation   83 (61.9%)   90 (67.2%)     88 (66.7%)          5.2 (-6.2 - 16.7)      
cl A.1                                                     53 (39.6%)   55 (41.0%)     69 (52.3%)          1.5 (-10.3 - 13.2)     
  FMQ1                                                     22 (16.4%)   21 (15.7%)     37 (28.0%)          -0.7 (-9.5 - 8.0)      
  FMQ2                                                     24 (17.9%)   31 (23.1%)     33 (25.0%)          5.2 (-4.4 - 14.9)      
  FMQ3                                                     28 (20.9%)   25 (18.7%)     31 (23.5%)          -2.2 (-11.8 - 7.3)     
cl B.1                                                     35 (26.1%)   41 (30.6%)     36 (27.3%)          4.5 (-6.3 - 15.3)      
  FMQ1                                                     12 (9.0%)    17 (12.7%)     19 (14.4%)          3.7 (-3.7 - 11.2)      
  FMQ2                                                      9 (6.7%)    21 (15.7%)     20 (15.2%)           9.0 (1.5 - 16.4)      
  FMQ3                                                     19 (14.2%)   11 (8.2%)       7 (5.3%)           -6.0 (-13.5 - 1.5)     
cl B.2                                                     36 (26.9%)   33 (24.6%)     35 (26.5%)          -2.2 (-12.7 - 8.2)     
  FMQ1                                                     16 (11.9%)   15 (11.2%)     12 (9.1%)           -0.7 (-8.4 - 6.9)      
  FMQ2                                                     17 (12.7%)   12 (9.0%)      16 (12.1%)          -3.7 (-11.2 - 3.7)     
  FMQ3                                                     11 (8.2%)    13 (9.7%)      15 (11.4%)           1.5 (-5.3 - 8.3)      
cl C.2                                                     26 (19.4%)   39 (29.1%)     43 (32.6%)          9.7 (-0.5 - 19.9)      
  FMQ1                                                     11 (8.2%)    12 (9.0%)      19 (14.4%)           0.7 (-6.0 - 7.5)      
  FMQ2                                                     11 (8.2%)    15 (11.2%)     14 (10.6%)          3.0 (-4.1 - 10.1)      
  FMQ3                                                      8 (6.0%)    14 (10.4%)     14 (10.6%)          4.5 (-2.1 - 11.0)      
cl D.1                                                     51 (38.1%)   51 (38.1%)     60 (45.5%)          0.0 (-11.6 - 11.6)     
  FMQ1                                                     22 (16.4%)   22 (16.4%)     32 (24.2%)           0.0 (-8.9 - 8.9)      
  FMQ2                                                     24 (17.9%)   25 (18.7%)     33 (25.0%)          0.7 (-8.5 - 10.0)      
  FMQ3                                                     19 (14.2%)   24 (17.9%)     26 (19.7%)          3.7 (-5.0 - 12.5)      
cl D.2                                                     35 (26.1%)   46 (34.3%)     44 (33.3%)          8.2 (-2.7 - 19.2)      
  FMQ1                                                     11 (8.2%)    23 (17.2%)     17 (12.9%)           9.0 (1.1 - 16.9)      
  FMQ2                                                     18 (13.4%)   16 (11.9%)     18 (13.6%)          -1.5 (-9.5 - 6.5)      
  FMQ3                                                     11 (8.2%)    16 (11.9%)     15 (11.4%)          3.7 (-3.5 - 10.9)      

Function Details

make_table_11_rtables()

---

Required variables:

• df: USUBJID, AEBODSYS, AESER, DCSREAS, and the variables specified by arm_var, saffl_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"
fmqsc_var	(character) FMQ scope variable to use in table.	"FMQ01SC"
fmqnam_var	(character) FMQ reference name variable to use in table.	"FMQ01NAM"
fmq_scope	(character) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’.	"NARROW"
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.