FDA Table 6

Overview of Adverse Events, Safety Population, Pooled Analyses

gtsummary Table Setup

# Load package and data
library(cardinal)

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

# Output Table
make_table_06(df = adae, denominator = adsl, return_ard = FALSE)

Event	A: Drug X N = 134¹	B: Placebo N = 134¹	C: Combination N = 132¹
SAE	104 (78%)	101 (75%)	99 (75%)
SAEs with fatal outcome	76 (57%)	70 (52%)	75 (57%)
Life-threatening SAEs	9 (6.7%)	13 (9.7%)	19 (14%)
SAEs requiring hospitalization	24 (18%)	28 (21%)	30 (23%)
SAEs resulting in substantial disruption of normal life functions	28 (21%)	21 (16%)	23 (17%)
Congenital anomaly or birth defect	26 (19%)	27 (20%)	20 (15%)
Other	30 (22%)	37 (28%)	32 (24%)
AE leading to permanent discontinuation of study drug	75 (56%)	73 (54%)	83 (63%)
AE leading to dose modification of study drug	71 (53%)	86 (64%)	83 (63%)
AE leading to dose delay of study drug	20 (15%)	28 (21%)	30 (23%)
AE leading to interruption of study drug	4 (3.0%)	4 (3.0%)	3 (2.3%)
AE leading to reduction of study drug	46 (34%)	46 (34%)	51 (39%)
Other	34 (25%)	48 (36%)	46 (35%)
Any AE	122 (91%)	123 (92%)	120 (91%)
MILD	88 (66%)	95 (71%)	102 (77%)
MODERATE	99 (74%)	100 (75%)	103 (78%)
SEVERE	91 (68%)	90 (67%)	93 (70%)
¹ n (%)

Function Details

`make_table_06()`

Required variables:

df: The variables specified by id_var and arm_var.
denominator : The variables specified by saffl_var, arm_var, sae_var, sae_cat_vars, disc_var, dose_mod_var, and sev_var.

Argument	Description	Default
`df`	(`data.frame`) Dataset (typically ADAE) required to build the table.	No default
`return_ard`	(`flag`) Whether an ARD should be returned.	`TRUE`
`denominator`	(`character`) Alternative dataset (typically ADSL) used only to calculate column counts.	No default
`id_var`	(`character`) Identifier variable used to count the participants within each category.	`"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"`
`sae_var`	(`character`) Flag variable used to indicate whether an adverse event is serious or not.	`"AESER"`
`sae_cat_vars`	(`character list`) Named list of flag variables for categories of serious adverse events. List names represent the labels in the table.	`"list("SAEs with fatal outcome" = "AESDTH", "Life-threatening SAEs" = "AESLIFE", "SAEs requiring hospitalization" = "AESHOSP", "SAEs resulting in substantial disruption of normal life functions" = "AESDISAB", "Congenital anomaly or birth defect" = "AESCONG", "Other" = "AESMIE")"`
`disc_var`	(`character`) Flag variable used to indicate whether the subject was discontinued from the study as result of an adverse event.	`"AEACNOTH"`
`dose_mod_var`	(`character`) Flag variable used to indicate whether the dose was modified as result of an adverse event.	`"AEACN"`
`dose_mod_cat_labels`	(`character list`) Named list of labels. Names may be “DRUG INTERRUPTED”, “DOSE REDUCED”, “DOSE RATE REDUCED”, “DOSE INCREASED”.	`"list("DRUG INTERRUPTED" = "AE leading to interruption of study drug", "DOSE REDUCED" = "AE leading to reduction of study drug" , "DOSE RATE REDUCED" = "AE leading to dose delay of study drug", "DOSE INCREASED" = "Other")"`
`sev_var`	(`character`) Variable containing the severity of an adverse event.	`"AESEV"`
`na_level`	(`character`) String to represent missing values.	`"<Missing>"`

Source code for this function is available here.

ARD Setup

# Load package and data
library(cardinal)

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

# Create table & ARD
result <- make_table_06(df = adae, denominator = adsl)

# Output ARD
result$ard

[[1]]
[[1]][[1]]
[[1]][[1]]$tbl_hierarchical

{cards} data frame: 18 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    AESER            SAE hierarch…         n          n   104      104   <fn>                   stat_1
2     ARM    A: Drug X    AESER            SAE hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X    AESER            SAE hierarch…         p          % 0.776       78   <fn>                   stat_1
4     ARM    B: Place…    AESER            SAE hierarch…         n          n   101      101   <fn>                   stat_2
5     ARM    B: Place…    AESER            SAE hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…    AESER            SAE hierarch…         p          % 0.754       75   <fn>                   stat_2
7     ARM    C: Combi…    AESER            SAE hierarch…         n          n    99       99   <fn>                   stat_3
8     ARM    C: Combi…    AESER            SAE hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…    AESER            SAE hierarch…         p          %  0.75       75   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$`SAEs with fatal outcome`
[[1]]$`SAEs with fatal outcome`$tbl_hierarchical

{cards} data frame: 18 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   AESDTH      SAEs wit… hierarch…         n          n    76       76   <fn>                   stat_1
2     ARM    A: Drug X   AESDTH      SAEs wit… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X   AESDTH      SAEs wit… hierarch…         p          % 0.567       57   <fn>                   stat_1
4     ARM    B: Place…   AESDTH      SAEs wit… hierarch…         n          n    70       70   <fn>                   stat_2
5     ARM    B: Place…   AESDTH      SAEs wit… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…   AESDTH      SAEs wit… hierarch…         p          % 0.522       52   <fn>                   stat_2
7     ARM    C: Combi…   AESDTH      SAEs wit… hierarch…         n          n    75       75   <fn>                   stat_3
8     ARM    C: Combi…   AESDTH      SAEs wit… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…   AESDTH      SAEs wit… hierarch…         p          % 0.568       57   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$`Life-threatening SAEs`
[[1]]$`Life-threatening SAEs`$tbl_hierarchical

{cards} data frame: 18 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  AESLIFE      Life-thr… hierarch…         n          n     9        9   <fn>                   stat_1
2     ARM    A: Drug X  AESLIFE      Life-thr… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X  AESLIFE      Life-thr… hierarch…         p          % 0.067      6.7   <fn>                   stat_1
4     ARM    B: Place…  AESLIFE      Life-thr… hierarch…         n          n    13       13   <fn>                   stat_2
5     ARM    B: Place…  AESLIFE      Life-thr… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…  AESLIFE      Life-thr… hierarch…         p          % 0.097      9.7   <fn>                   stat_2
7     ARM    C: Combi…  AESLIFE      Life-thr… hierarch…         n          n    19       19   <fn>                   stat_3
8     ARM    C: Combi…  AESLIFE      Life-thr… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…  AESLIFE      Life-thr… hierarch…         p          % 0.144       14   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$`SAEs requiring hospitalization`
[[1]]$`SAEs requiring hospitalization`$tbl_hierarchical

{cards} data frame: 18 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  AESHOSP      SAEs req… hierarch…         n          n    24       24   <fn>                   stat_1
2     ARM    A: Drug X  AESHOSP      SAEs req… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X  AESHOSP      SAEs req… hierarch…         p          % 0.179       18   <fn>                   stat_1
4     ARM    B: Place…  AESHOSP      SAEs req… hierarch…         n          n    28       28   <fn>                   stat_2
5     ARM    B: Place…  AESHOSP      SAEs req… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…  AESHOSP      SAEs req… hierarch…         p          % 0.209       21   <fn>                   stat_2
7     ARM    C: Combi…  AESHOSP      SAEs req… hierarch…         n          n    30       30   <fn>                   stat_3
8     ARM    C: Combi…  AESHOSP      SAEs req… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…  AESHOSP      SAEs req… hierarch…         p          % 0.227       23   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$`SAEs resulting in substantial disruption of normal life functions`
[[1]]$`SAEs resulting in substantial disruption of normal life functions`$tbl_hierarchical

{cards} data frame: 18 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 AESDISAB      SAEs res… hierarch…         n          n    28       28   <fn>                   stat_1
2     ARM    A: Drug X AESDISAB      SAEs res… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X AESDISAB      SAEs res… hierarch…         p          % 0.209       21   <fn>                   stat_1
4     ARM    B: Place… AESDISAB      SAEs res… hierarch…         n          n    21       21   <fn>                   stat_2
5     ARM    B: Place… AESDISAB      SAEs res… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place… AESDISAB      SAEs res… hierarch…         p          % 0.157       16   <fn>                   stat_2
7     ARM    C: Combi… AESDISAB      SAEs res… hierarch…         n          n    23       23   <fn>                   stat_3
8     ARM    C: Combi… AESDISAB      SAEs res… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi… AESDISAB      SAEs res… hierarch…         p          % 0.174       17   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$`Congenital anomaly or birth defect`
[[1]]$`Congenital anomaly or birth defect`$tbl_hierarchical

{cards} data frame: 18 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  AESCONG      Congenit… hierarch…         n          n    26       26   <fn>                   stat_1
2     ARM    A: Drug X  AESCONG      Congenit… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X  AESCONG      Congenit… hierarch…         p          % 0.194       19   <fn>                   stat_1
4     ARM    B: Place…  AESCONG      Congenit… hierarch…         n          n    27       27   <fn>                   stat_2
5     ARM    B: Place…  AESCONG      Congenit… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…  AESCONG      Congenit… hierarch…         p          % 0.201       20   <fn>                   stat_2
7     ARM    C: Combi…  AESCONG      Congenit… hierarch…         n          n    20       20   <fn>                   stat_3
8     ARM    C: Combi…  AESCONG      Congenit… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…  AESCONG      Congenit… hierarch…         p          % 0.152       15   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[1]]$Other
[[1]]$Other$tbl_hierarchical

{cards} data frame: 18 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   AESMIE          Other hierarch…         n          n    30       30   <fn>                   stat_1
2     ARM    A: Drug X   AESMIE          Other hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X   AESMIE          Other hierarch…         p          % 0.224       22   <fn>                   stat_1
4     ARM    B: Place…   AESMIE          Other hierarch…         n          n    37       37   <fn>                   stat_2
5     ARM    B: Place…   AESMIE          Other hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place…   AESMIE          Other hierarch…         p          % 0.276       28   <fn>                   stat_2
7     ARM    C: Combi…   AESMIE          Other hierarch…         n          n    32       32   <fn>                   stat_3
8     ARM    C: Combi…   AESMIE          Other hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi…   AESMIE          Other hierarch…         p          % 0.242       24   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3



[[2]]
[[2]]$tbl_hierarchical

{cards} data frame: 18 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 AEACNOTH      AE leadi… hierarch…         n          n    75       75   <fn>                   stat_1
2     ARM    A: Drug X AEACNOTH      AE leadi… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X AEACNOTH      AE leadi… hierarch…         p          %  0.56       56   <fn>                   stat_1
4     ARM    B: Place… AEACNOTH      AE leadi… hierarch…         n          n    73       73   <fn>                   stat_2
5     ARM    B: Place… AEACNOTH      AE leadi… hierarch…         N          N   134      134   <fn>                   stat_2
6     ARM    B: Place… AEACNOTH      AE leadi… hierarch…         p          % 0.545       54   <fn>                   stat_2
7     ARM    C: Combi… AEACNOTH      AE leadi… hierarch…         n          n    83       83   <fn>                   stat_3
8     ARM    C: Combi… AEACNOTH      AE leadi… hierarch…         N          N   132      132   <fn>                   stat_3
9     ARM    C: Combi… AEACNOTH      AE leadi… hierarch…         p          % 0.629       63   <fn>                   stat_3
10   <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
11   <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
12   <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
13   <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
14   <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
15   <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
16   <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
17   <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
18   <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3


[[3]]
[[3]]$tbl_hierarchical

{cards} data frame: 54 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    AEACN      AE leadi… hierarch…         n          n    20       20   <fn>                   stat_1
2     ARM    A: Drug X    AEACN      AE leadi… hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X    AEACN      AE leadi… hierarch…         p          % 0.149       15   <fn>                   stat_1
4     ARM    A: Drug X    AEACN      AE leadi… hierarch…         n          n     4        4   <fn>                   stat_1
5     ARM    A: Drug X    AEACN      AE leadi… hierarch…         N          N   134      134   <fn>                   stat_1
6     ARM    A: Drug X    AEACN      AE leadi… hierarch…         p          %  0.03      3.0   <fn>                   stat_1
7     ARM    A: Drug X    AEACN      AE leadi… hierarch…         n          n    46       46   <fn>                   stat_1
8     ARM    A: Drug X    AEACN      AE leadi… hierarch…         N          N   134      134   <fn>                   stat_1
9     ARM    A: Drug X    AEACN      AE leadi… hierarch…         p          % 0.343       34   <fn>                   stat_1
10    ARM    A: Drug X    AEACN          Other hierarch…         n          n    34       34   <fn>                   stat_1

ℹ 44 more rows

ℹ Use `print(n = ...)` to see more rows



[[4]]
[[4]]$tbl_hierarchical

{cards} data frame: 45 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                        AESEV           MILD hierarch…         n          n    88       88   <fn>                   stat_1
2     ARM    A: Drug X                        AESEV           MILD hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X                        AESEV           MILD hierarch…         p          % 0.657       66   <fn>                   stat_1
4     ARM    A: Drug X                        AESEV       MODERATE hierarch…         n          n    99       99   <fn>                   stat_1
5     ARM    A: Drug X                        AESEV       MODERATE hierarch…         N          N   134      134   <fn>                   stat_1
6     ARM    A: Drug X                        AESEV       MODERATE hierarch…         p          % 0.739       74   <fn>                   stat_1
7     ARM    A: Drug X                        AESEV         SEVERE hierarch…         n          n    91       91   <fn>                   stat_1
8     ARM    A: Drug X                        AESEV         SEVERE hierarch…         N          N   134      134   <fn>                   stat_1
9     ARM    A: Drug X                        AESEV         SEVERE hierarch…         p          % 0.679       68   <fn>                   stat_1
10    ARM    A: Drug X ..ard_hierarchical_overall..           TRUE hierarch…         n          n   122      122   <fn>                   stat_1

ℹ 35 more rows
ℹ Use `print(n = ...)` to see more rows

rtables Table Setup

# Load package and 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_06_rtables(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

                                                                       A: Drug X    B: Placebo    C: Combination   Risk Difference (%) (95% CI)
Event                                                                   (N=134)       (N=134)        (N=132)                 (N=268)           
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
SAE                                                                   104 (77.6%)   101 (75.4%)     99 (75.0%)          -2.2 (-12.4 - 7.9)     
  SAEs with fatal outcome                                             76 (56.7%)    70 (52.2%)      75 (56.8%)          -4.5 (-16.4 - 7.4)     
  Life-threatening SAEs                                                9 (6.7%)      13 (9.7%)      19 (14.4%)           3.0 (-3.6 - 9.5)      
  SAEs requiring hospitalization                                      24 (17.9%)    28 (20.9%)      30 (22.7%)          3.0 (-6.5 - 12.4)      
  SAEs resulting in substantial disruption of normal life functions   28 (20.9%)    21 (15.7%)      23 (17.4%)          -5.2 (-14.5 - 4.0)     
  Congenital anomaly or birth defect                                  26 (19.4%)    27 (20.1%)      20 (15.2%)          0.7 (-8.8 - 10.3)      
  Other                                                               30 (22.4%)    37 (27.6%)      32 (24.2%)          5.2 (-5.1 - 15.6)      
AE leading to permanent discontinuation of study drug                 27 (20.1%)    26 (19.4%)      30 (22.7%)          -0.7 (-10.3 - 8.8)     
AE leading to dose modification of study drug                         71 (53.0%)    86 (64.2%)      83 (62.9%)          11.2 (-0.5 - 22.9)     
  AE leading to interruption of study drug                             4 (3.0%)      4 (3.0%)        3 (2.3%)            0.0 (-4.1 - 4.1)      
  AE leading to reduction of study drug                               46 (34.3%)    46 (34.3%)      51 (38.6%)          0.0 (-11.4 - 11.4)     
  AE leading to dose delay of study drug                              20 (14.9%)    28 (20.9%)      30 (22.7%)          6.0 (-3.2 - 15.1)      
  Other                                                               34 (25.4%)    48 (35.8%)      46 (34.8%)          10.4 (-0.5 - 21.4)     
Any AE                                                                122 (91.0%)   123 (91.8%)    120 (90.9%)           0.7 (-6.0 - 7.5)      
  MILD                                                                 7 (5.2%)      9 (6.7%)        4 (3.0%)            1.5 (-4.2 - 7.2)      
  MODERATE                                                            24 (17.9%)    24 (17.9%)      23 (17.4%)           0.0 (-9.2 - 9.2)      
  SEVERE                                                              91 (67.9%)    90 (67.2%)      93 (70.5%)         -0.7 (-12.0 - 10.5)

Function Details

`make_table_06_rtables()`

Required variables:

adae: USUBJID, TRTEMFL, AESEV, AESER, AESDTH, AESLIFE, AESHOSP, AESDISAB, AESCONG, AESMIE, AEACN, and the variables specified by 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`
`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"`
`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.