FDA Table 08

All Individual Patient Deaths, Safety Population, Pooled Analyses

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Setup

# Load libraries & data -------------------------------------
library(dplyr)
library(cards)
library(gtsummary)

adae <- pharmaverseadam::adae
adex <- pharmaverseadam::adex

# Pre-processing --------------------------------------------
# deaths
adae <- adae |>
  filter(
    # safety population
    SAFFL == "Y",
    # deaths
    DTHFL == "Y"
  ) |>
  # select variables from `adae` to include in final result
  select(USUBJID, TRT01A, AGE, SEX, DTHADY, DTHCAUS) |>
  # derive formatted "Age/Gender" column values
  mutate(
    AGE_SEX = paste(AGE, SEX, sep = "/")
  ) |>
  # keep one row per unique ID
  distinct(USUBJID, DTHCAUS, DTHADY, .keep_all = TRUE)

# dosing
adex <- adex |>
  filter(
    # safety population
    SAFFL == "Y",
    # total dosages
    PARAMCD == "TDOSE"
  ) |>
  # select variables from `adex` to include in final result
  select(USUBJID, AVAL, TRTSDT, TRTEDT) |>
  mutate(
    # derive dosage duration
    DOSDUR = (TRTEDT - TRTSDT + 1) |> as.character(),
    # format dosage values
    DOSAGE = paste0(AVAL, " mg")
  )

# combine all data
data <- left_join(adae, adex, by = "USUBJID") |>
  select(TRT01A, USUBJID, AGE_SEX, DOSAGE, DOSDUR, DTHADY, DTHCAUS) |>
  arrange()

Build Table

tbl <- as_gtsummary(data) |>
  # set table header labels
  modify_header(
    TRT01A = "**Study Arm**",
    USUBJID = "**Patient ID**",
    AGE_SEX = "**Age/**  \n **Gender**",
    DOSAGE = "**Dosage**",
    DOSDUR = "**Dosing**  \n **Duration**  \n **(Days)**",
    DTHADY = "**Study**  \n **Day of**  \n **Death**",
    DTHCAUS = "**Cause of Death**"
  ) |>
  # align all columns left
  modify_column_alignment(everything(), align = "left")

tbl

Build ARD

# For this table we do not build an ARD since we are returning the complete
# dataset as our result, so there are no statistics to display in an ARD.
# The full unformatted dataset (`data`) can be used instead if needed
data

# A tibble: 3 × 7
  TRT01A              USUBJID     AGE_SEX DOSAGE  DOSDUR DTHADY DTHCAUS              
  <chr>               <chr>       <chr>   <chr>   <chr>   <dbl> <chr>                
1 Xanomeline Low Dose 01-701-1211 76/F    3186 mg 59         61 SUDDEN DEATH         
2 Placebo             01-704-1445 75/M    0 mg    175       175 COMPLETED SUICIDE    
3 Placebo             01-710-1083 89/F    0 mg    11         12 MYOCARDIAL INFARCTION