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Subjects With Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)

FDA Table 14

table
FDA
safety
adverse events

FDA IG Shell

FDA IG example table shell

Programming Notes

Background and Instructions

Table 14: Subjects With Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X) presents the entire table of AEs by SOC, while Table 15: Subjects With Common Adverse Events shows common AEs by PT. Review of PTs by SOC can elucidate potential imbalances within the same body system that may not be as apparent when looking at individual AEs.

Customization

The full list of PTs to be included in this table may lead to a multi-page table and affect readability. In this case, the review team could consider displaying this table using a frequency cutoff for ease of review. The full table containing all data can be reviewed in the spreadsheet provided by CDS.

Output

  • Full Code
  • Table
  • ARD
Code
# FDA TABLE 14 ---------------------------------------------------------------
# Self-contained template. Run top-to-bottom to build the objects below.
# Used by tests via run_template() and published in the catalog.

library(dplyr)
library(cards)
library(gtsummary)

adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae

# Pre-processing --------------------------------------------
adsl <- adsl |>
  filter(SAFFL == "Y") # safety population

# for display purpose showing only bottom 5 SOCs
sliced_data <- adae |>
  count(AESOC) |>
  slice_min(order_by = n, n = 5) |>
  pull(AESOC)

data <- adae |>
  filter(AESOC %in% sliced_data)

ard <- ard_stack_hierarchical(
  data,
  variables = c(AESOC, AEDECOD),
  by = TRT01A,
  id = USUBJID,
  denominator = adsl
)

# create table using ARD-first approach (ARD -> table)
tbl <-
  tbl_ard_hierarchical(
    ard,
    variables = c(AESOC, AEDECOD),
    by = TRT01A,
    # add custom variable labels
    label = list(
      AESOC = "System Organ Class",
      AEDECOD = "Preferred Term"
    )
  )


ard <- gtsummary::gather_ard(tbl)
Code
tbl
System Organ Class
    Preferred Term
Placebo
N = 861
Xanomeline High Dose
N = 721
Xanomeline Low Dose
N = 961
CONGENITAL, FAMILIAL AND GENETIC DISORDERS 0 (0.0%) 2 (2.8%) 1 (1.0%)
    VENTRICULAR SEPTAL DEFECT 0 (0.0%) 2 (2.8%) 1 (1.0%)
HEPATOBILIARY DISORDERS 1 (1.2%) 0 (0.0%) 0 (0.0%)
    HYPERBILIRUBINAEMIA 1 (1.2%) 0 (0.0%) 0 (0.0%)
IMMUNE SYSTEM DISORDERS 0 (0.0%) 1 (1.4%) 1 (1.0%)
    HYPERSENSITIVITY 0 (0.0%) 0 (0.0%) 1 (1.0%)
    SEASONAL ALLERGY 0 (0.0%) 1 (1.4%) 0 (0.0%)
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) 0 (0.0%) 1 (1.4%) 2 (2.1%)
    COLON CANCER 0 (0.0%) 0 (0.0%) 1 (1.0%)
    MALIGNANT FIBROUS HISTIOCYTOMA 0 (0.0%) 0 (0.0%) 1 (1.0%)
    PROSTATE CANCER 0 (0.0%) 1 (1.4%) 0 (0.0%)
SOCIAL CIRCUMSTANCES 0 (0.0%) 1 (1.4%) 0 (0.0%)
    ALCOHOL USE 0 (0.0%) 1 (1.4%) 0 (0.0%)
1 n (%)
Code
withr::local_options(width = 9999, tibble.print_max = Inf)
print(ard, columns = "all")
$tbl_ard_hierarchical
# An ARD data frame: 126 × 15
    group1 group1_level         group2 group2_level                                                        variable variable_level                                                      context      stat_name stat_label     stat stat_fmt fmt_fun warning error  gts_column
    <chr>  <list>               <chr>  <list>                                                              <chr>    <list>                                                              <chr>        <chr>     <chr>        <list> <list>   <list>  <list>  <list> <chr>     
  1 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Placebo                                                             tabulate     n         n           86      86       0       <NULL>  <NULL> stat_1    
  2 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Placebo                                                             tabulate     N         N          254      254      0       <NULL>  <NULL> stat_1    
  3 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Placebo                                                             tabulate     p         %            0.339  33.9     <fn>    <NULL>  <NULL> stat_1    
  4 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline High Dose                                                tabulate     n         n           72      72       0       <NULL>  <NULL> stat_2    
  5 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline High Dose                                                tabulate     N         N          254      254      0       <NULL>  <NULL> stat_2    
  6 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline High Dose                                                tabulate     p         %            0.283  28.3     <fn>    <NULL>  <NULL> stat_2    
  7 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline Low Dose                                                 tabulate     n         n           96      96       0       <NULL>  <NULL> stat_3    
  8 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline Low Dose                                                 tabulate     N         N          254      254      0       <NULL>  <NULL> stat_3    
  9 <NA>   <NULL>               <NA>   <NULL>                                                              TRT01A   Xanomeline Low Dose                                                 tabulate     p         %            0.378  37.8     <fn>    <NULL>  <NULL> stat_3    
 10 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 11 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 12 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 13 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical n         n            2      2        0       <NULL>  <NULL> stat_2    
 14 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 15 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical p         %            0.0278 2.8      <fn>    <NULL>  <NULL> stat_2    
 16 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 17 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 18 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
 19 TRT01A Placebo              AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 20 TRT01A Placebo              AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 21 TRT01A Placebo              AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 22 TRT01A Xanomeline High Dose AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical n         n            2      2        0       <NULL>  <NULL> stat_2    
 23 TRT01A Xanomeline High Dose AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 24 TRT01A Xanomeline High Dose AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical p         %            0.0278 2.8      <fn>    <NULL>  <NULL> stat_2    
 25 TRT01A Xanomeline Low Dose  AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 26 TRT01A Xanomeline Low Dose  AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 27 TRT01A Xanomeline Low Dose  AESOC  CONGENITAL, FAMILIAL AND GENETIC DISORDERS                          AEDECOD  VENTRICULAR SEPTAL DEFECT                                           hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
 28 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical n         n            1      1        0       <NULL>  <NULL> stat_1    
 29 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 30 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical p         %            0.0116 1.2      <fn>    <NULL>  <NULL> stat_1    
 31 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical n         n            0      0        0       <NULL>  <NULL> stat_2    
 32 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 33 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_2    
 34 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
 35 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 36 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    HEPATOBILIARY DISORDERS                                             hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
 37 TRT01A Placebo              AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical n         n            1      1        0       <NULL>  <NULL> stat_1    
 38 TRT01A Placebo              AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 39 TRT01A Placebo              AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical p         %            0.0116 1.2      <fn>    <NULL>  <NULL> stat_1    
 40 TRT01A Xanomeline High Dose AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical n         n            0      0        0       <NULL>  <NULL> stat_2    
 41 TRT01A Xanomeline High Dose AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 42 TRT01A Xanomeline High Dose AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_2    
 43 TRT01A Xanomeline Low Dose  AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
 44 TRT01A Xanomeline Low Dose  AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 45 TRT01A Xanomeline Low Dose  AESOC  HEPATOBILIARY DISORDERS                                             AEDECOD  HYPERBILIRUBINAEMIA                                                 hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
 46 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 47 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 48 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 49 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
 50 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 51 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
 52 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 53 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 54 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    IMMUNE SYSTEM DISORDERS                                             hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
 55 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 56 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 57 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 58 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical n         n            0      0        0       <NULL>  <NULL> stat_2    
 59 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 60 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_2    
 61 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 62 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 63 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  HYPERSENSITIVITY                                                    hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
 64 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 65 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 66 TRT01A Placebo              AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 67 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
 68 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 69 TRT01A Xanomeline High Dose AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
 70 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
 71 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 72 TRT01A Xanomeline Low Dose  AESOC  IMMUNE SYSTEM DISORDERS                                             AEDECOD  SEASONAL ALLERGY                                                    hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
 73 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 74 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 75 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 76 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
 77 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 78 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
 79 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical n         n            2      2        0       <NULL>  <NULL> stat_3    
 80 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 81 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) hierarchical p         %            0.0208 2.1      <fn>    <NULL>  <NULL> stat_3    
 82 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 83 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 84 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 85 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical n         n            0      0        0       <NULL>  <NULL> stat_2    
 86 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 87 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_2    
 88 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 89 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 90 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  COLON CANCER                                                        hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
 91 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
 92 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
 93 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
 94 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical n         n            0      0        0       <NULL>  <NULL> stat_2    
 95 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
 96 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_2    
 97 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical n         n            1      1        0       <NULL>  <NULL> stat_3    
 98 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
 99 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  MALIGNANT FIBROUS HISTIOCYTOMA                                      hierarchical p         %            0.0104 1.0      <fn>    <NULL>  <NULL> stat_3    
100 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
101 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
102 TRT01A Placebo              AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
103 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
104 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
105 TRT01A Xanomeline High Dose AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
106 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
107 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
108 TRT01A Xanomeline Low Dose  AESOC  NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) AEDECOD  PROSTATE CANCER                                                     hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
109 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
110 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
111 TRT01A Placebo              <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
112 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
113 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
114 TRT01A Xanomeline High Dose <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
115 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
116 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
117 TRT01A Xanomeline Low Dose  <NA>   <NULL>                                                              AESOC    SOCIAL CIRCUMSTANCES                                                hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
118 TRT01A Placebo              AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical n         n            0      0        0       <NULL>  <NULL> stat_1    
119 TRT01A Placebo              AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical N         N           86      86       0       <NULL>  <NULL> stat_1    
120 TRT01A Placebo              AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_1    
121 TRT01A Xanomeline High Dose AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical n         n            1      1        0       <NULL>  <NULL> stat_2    
122 TRT01A Xanomeline High Dose AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical N         N           72      72       0       <NULL>  <NULL> stat_2    
123 TRT01A Xanomeline High Dose AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical p         %            0.0139 1.4      <fn>    <NULL>  <NULL> stat_2    
124 TRT01A Xanomeline Low Dose  AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical n         n            0      0        0       <NULL>  <NULL> stat_3    
125 TRT01A Xanomeline Low Dose  AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical N         N           96      96       0       <NULL>  <NULL> stat_3    
126 TRT01A Xanomeline Low Dose  AESOC  SOCIAL CIRCUMSTANCES                                                AEDECOD  ALCOHOL USE                                                         hierarchical p         %            0      0.0      <fn>    <NULL>  <NULL> stat_3    
Source Code
---
title: Subjects With Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)
subtitle: FDA Table 14
categories: [table, FDA, safety, adverse events]
---

::::: columns

:::: {.column width="52%"}
### FDA IG Shell

![](ig_shell.png){fig-alt="FDA IG example table shell" .lightbox width=100%}

### Programming Notes

**Background and Instructions**

Table 14: Subjects With Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X) presents the entire table of AEs by SOC, while Table 15: Subjects With Common Adverse Events shows common AEs by PT. Review of PTs by SOC can elucidate potential imbalances within the same body system that may not be as apparent when looking at individual AEs.

**Customization**

The full list of PTs to be included in this table may lead to a multi-page table and affect readability. In this case, the review team could consider displaying this table using a frequency cutoff for ease of review. The full table containing all data can be reviewed in the spreadsheet provided by CDS.

::::

:::: {.column width="4%"}
::::

:::: {.column width="44%"}
### Output

```{r out-result, echo=FALSE, fig.align='center', out.width='100%'}
knitr::include_graphics("result.png")
```

::::

:::::

::: panel-tabset
## Full Code

```{r fullcode, file="../../../inst/templates/fda-table_14.R", message=FALSE, warning=FALSE, results='hide'}
```

## Table

```{r tbl}
tbl
```

## ARD

```{r ard, message=FALSE, warning=FALSE}
withr::local_options(width = 9999, tibble.print_max = Inf)
print(ard, columns = "all")
```

:::
 
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