LSFAE04

Listing of Adverse Events Leading to Death

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# Program Name:              lsfae04.R

# Prep environment

library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(rlistings)
library(junco)
library(stringi)
library(junco)

# Define script level parameters

tblid <- "LSFAE04"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
key_cols <- c("COL0", "COL1", "COL2")
disp_cols <- paste0("COL", 0:10)
concat_sep <- " / "
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
# Parameter to control whether time should be displayed
include_time <- TRUE

# Process data

adae <- pharmaverseadamjnj::adae %>%
  filter(!!rlang::sym(popfl) == "Y" & AEOUT == "FATAL")

lsting <- adae %>%
  mutate(
    AGE = explicit_na(as.character(AGE), ""),
    SEX = explicit_na(SEX, ""),
    RACE_DECODE = explicit_na(RACE_DECODE, ""),
    DOSEON = explicit_na(as.character(DOSEON), ""),
    DOSEU = explicit_na(DOSEU, ""),
    DOSEDY = explicit_na(as.character(DOSEDY), ""),
    AEDECOD = explicit_na(AEDECOD, ""),
    AETERM = ifelse(
      is.na(AETERM),
      "",
      stringi::stri_trans_totitle(gsub("\\$", "", AETERM))
    ),
    ASTDT = ifelse(
      nchar(as.character(ASTDT)) == 10,
      toupper(format(ASTDT, "%d%b%Y")),
      ""
    ),
    ASTTM = ifelse(
      include_time & !is.na(ASTDTM),
      substr(as.character(ASTDTM), 12, 16),
      ""
    ),
    ASTDYN = ifelse(!is.na(ASTDY), ASTDY, NA),
    ASTDY = ifelse(!is.na(ASTDY), ASTDY, ""),
    ASTDTFS = ifelse(!is.na(ASTDTF), "*", ""),
    AENDT = explicit_na(as.character(AENDT), ""),
    AENDT = ifelse(
      nchar(AENDT) == 10,
      toupper(format(as.Date(AENDT), "%d%b%Y")),
      ""
    ),
    AENTM = ifelse(
      include_time & !is.na(AENDTM),
      substr(as.character(AENDTM), 12, 16),
      ""
    ),
    AENDY = ifelse(!is.na(AENDY), AENDY, ""),
    AENDTFS = ifelse(!is.na(AENDTF), "*", ""),
    AEOUTC = explicit_na(AEOUT_DECODE, ""),
    # Optional Variable: COL10/AESEV/AETOXGR
    # AESEV = explicit_na(AESEV,""),
    AETOXGR = explicit_na(AETOXGR, ""),
    AESER_DECODE = explicit_na(AESER_DECODE, ""),
    COL0 = explicit_na(.data[[trtvar]], ""),
    COL1 = explicit_na(USUBJID, ""),
    COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
    COL3 = paste(paste0(DOSEON, " ", DOSEU), DOSEDY, sep = concat_sep),
    COL4 = paste(AEDECOD, AETERM, sep = concat_sep),
    COL5 = ifelse(!is.na(TRTEMFL), "Yes", "No"),
    COL6 = case_when(
      ASTDT == "" ~ "",
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")"),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")"),
      ASTDT != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, " (", ASTDY, ")", ASTDTFS),
      ASTDT != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, " (", ASTDY, ")"),
    ),
    COL7 = case_when(
      AENDT == "" ~ "",
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")"),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")"),
      AENDT != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, " (", AENDY, ")", AENDTFS),
      AENDT != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, " (", AENDY, ")"),
    ),
    # Optional Column: COL8/AEACN
    COL8 = explicit_na(AEACN_DECODE, ""),
    COL9 = explicit_na(AEREL_DECODE, ""),
    # Optional Variable: COL10/AESEV/AETOXGR
    # COL10 = paste(AESEV, AESER, sep = concat_sep)
    COL10 = paste(AETOXGR, AESER_DECODE, sep = concat_sep)
  ) %>%
  arrange(
    COL0,
    COL1,
    COL2,
    !is.na(ASTDYN),
    ASTDYN,
    if (include_time) ASTDTM else ASTDT,
    AEDECOD,
    AETERM
  )

lsting <- var_relabel(
  lsting,
  COL0 = "Treatment Group",
  COL1 = "Subject ID",
  COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
  COL3 = paste(
    "Onset Dose (unit)",
    "Day of Last Dose~[super a,b]",
    sep = concat_sep
  ),
  COL4 = paste("Preferred Term", "Reported Term", sep = concat_sep),
  COL5 = "TE?",
  COL6 = if (include_time) {
    paste("Start Date", "Time (Study Day~[super b])", sep = concat_sep)
  } else {
    "Start Date (Study Day~[super b])"
  },
  COL7 = if (include_time) {
    paste("End Date", "Time (Study Day~[super b])", sep = concat_sep)
  } else {
    "End Date (Study Day~[super b])"
  },
  # Optional Column: COL8/AEACN
  COL8 = "Action Taken With Study Treatment",
  COL9 = "Relationship to Study Treatment~[super c]",
  # Optional Variable: COL10/AESEV/AETOXGR
  # COL10 = paste("Severity", "Serious", sep = concat_sep)
  COL10 = paste("Toxicity Grade", "Serious", sep = concat_sep)
)

# Build listing

result <- rlistings::as_listing(
  df = lsting,
  key_cols = key_cols,
  disp_cols = disp_cols
)

# Add titles and footnotes

result <- set_titles(result, tab_titles)

# Output listing

tt_to_tlgrtf(string_map = string_map, tt = head(result, 100), file = fileid, orientation = "landscape")

LSFAE04: Listing of Adverse Events Leading to Death; Safety Analysis Set (Study jjcs - core)
Treatment Group	Subject ID	Age (years) / Sex / Race	Onset Dose (unit) / Day of Last Dosea,b	Preferred Term / Reported Term	TE?	Start Date / Time (Study Dayb)	End Date / Time (Study Dayb)	Action Taken With Study Treatment	Relationship to Study Treatmentc	Toxicity Grade / Serious
Xanomeline Low Dose	01-701-1211	76 / F / Other	10 mg / 37	SUDDEN DEATH / Sudden Death	Yes	14JAN2013 / 00:00 (61)	14JAN2013 / 23:59 (61)	Dose Reduced	Not Related	1 / Yes
Placebo	01-710-1083	89 / F / White	10 mg / 37	MYOCARDIAL INFARCTION / Myocardial Infarction	Yes	02AUG2013 / 00:00 (12)	02AUG2013 / 23:59 (12)	Dose Rate Reduced	Possible	1 / Yes

Key: *=imputed date, day, or duration
a Study day of last administration of [study treatment] prior to or on AE start date.
b Study day is relative to [the start of [study treatment]].
c Relationship is assessed by the investigator.
Note: Adverse events are coded using MedDRA version 26.0; toxicity grade is evaluated according to NCI-CTCAE version 5.0..
[lsfae04.docx][/usr/lib/rstudio-server/bin/quarto/share/rmd/rmd.R] 12JAN2026, 16:09

Download RTF file

--- title: LSFAE04 subtitle: Listing of Adverse Events Leading to Death --- ------------------------------------------------------------------------ {{< include ../../_utils/envir_hook.qmd >}} ```{r setup, echo = FALSE, warning = FALSE, message = FALSE} options(docx.add_datetime = FALSE, tidytlg.add_datetime = FALSE) envsetup_config_name <- "default" # Path to the combined config file envsetup_file_path <- file.path("../..", "envsetup.yml") Sys.setenv(ENVSETUP_ENVIRON = '') library(envsetup) loaded_config <- config::get(config = envsetup_config_name, file = envsetup_file_path) envsetup::rprofile(loaded_config) dpscomp <- compound dpspdr <- paste(protocol,dbrelease,rpteff,sep="__") aptcomp <- compound aptpdr <- paste(protocol,dbrelease,rpteff,sep="__") ###### Study specific updates (formerly in envre) dpscomp <- "standards" dpspdr <- "jjcs__NULL__jjcs - core" apt <- FALSE library(junco) default_str_map <- rbind(default_str_map, c("&ctcae", "5.0")) ``` ## Output :::: panel-tabset ## {{< fa regular file-lines sm fw >}} Preview ```{r variant1, results='hide', warning = FALSE, message = FALSE} # Program Name: lsfae04.R # Prep environment library(envsetup) library(tern) library(dplyr) library(rtables) library(rlistings) library(junco) library(stringi) library(junco) # Define script level parameters tblid <- "LSFAE04" fileid <- tblid popfl <- "SAFFL" trtvar <- "TRT01A" key_cols <- c("COL0", "COL1", "COL2") disp_cols <- paste0("COL", 0:10) concat_sep <- " / " tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map # Parameter to control whether time should be displayed include_time <- TRUE # Process data adae <- pharmaverseadamjnj::adae %>% filter(!!rlang::sym(popfl) == "Y" & AEOUT == "FATAL") lsting <- adae %>% mutate( AGE = explicit_na(as.character(AGE), ""), SEX = explicit_na(SEX, ""), RACE_DECODE = explicit_na(RACE_DECODE, ""), DOSEON = explicit_na(as.character(DOSEON), ""), DOSEU = explicit_na(DOSEU, ""), DOSEDY = explicit_na(as.character(DOSEDY), ""), AEDECOD = explicit_na(AEDECOD, ""), AETERM = ifelse( is.na(AETERM), "", stringi::stri_trans_totitle(gsub("\\$", "", AETERM)) ), ASTDT = ifelse( nchar(as.character(ASTDT)) == 10, toupper(format(ASTDT, "%d%b%Y")), "" ), ASTTM = ifelse( include_time & !is.na(ASTDTM), substr(as.character(ASTDTM), 12, 16), "" ), ASTDYN = ifelse(!is.na(ASTDY), ASTDY, NA), ASTDY = ifelse(!is.na(ASTDY), ASTDY, ""), ASTDTFS = ifelse(!is.na(ASTDTF), "*", ""), AENDT = explicit_na(as.character(AENDT), ""), AENDT = ifelse( nchar(AENDT) == 10, toupper(format(as.Date(AENDT), "%d%b%Y")), "" ), AENTM = ifelse( include_time & !is.na(AENDTM), substr(as.character(AENDTM), 12, 16), "" ), AENDY = ifelse(!is.na(AENDY), AENDY, ""), AENDTFS = ifelse(!is.na(AENDTF), "*", ""), AEOUTC = explicit_na(AEOUT_DECODE, ""), # Optional Variable: COL10/AESEV/AETOXGR # AESEV = explicit_na(AESEV,""), AETOXGR = explicit_na(AETOXGR, ""), AESER_DECODE = explicit_na(AESER_DECODE, ""), COL0 = explicit_na(.data[[trtvar]], ""), COL1 = explicit_na(USUBJID, ""), COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep), COL3 = paste(paste0(DOSEON, " ", DOSEU), DOSEDY, sep = concat_sep), COL4 = paste(AEDECOD, AETERM, sep = concat_sep), COL5 = ifelse(!is.na(TRTEMFL), "Yes", "No"), COL6 = case_when( ASTDT == "" ~ "", include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS != "" ~ paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")", ASTDTFS), include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS == "" ~ paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")"), include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS != "" ~ paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")", ASTDTFS), include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS == "" ~ paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")"), ASTDT != "" & ASTDY != "" & ASTDTFS != "" ~ paste0(ASTDT, " (", ASTDY, ")", ASTDTFS), ASTDT != "" & ASTDY != "" & ASTDTFS == "" ~ paste0(ASTDT, " (", ASTDY, ")"), ), COL7 = case_when( AENDT == "" ~ "", include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS != "" ~ paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")", AENDTFS), include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS == "" ~ paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")"), include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS != "" ~ paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")", AENDTFS), include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS == "" ~ paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")"), AENDT != "" & AENDY != "" & AENDTFS != "" ~ paste0(AENDT, " (", AENDY, ")", AENDTFS), AENDT != "" & AENDY != "" & AENDTFS == "" ~ paste0(AENDT, " (", AENDY, ")"), ), # Optional Column: COL8/AEACN COL8 = explicit_na(AEACN_DECODE, ""), COL9 = explicit_na(AEREL_DECODE, ""), # Optional Variable: COL10/AESEV/AETOXGR # COL10 = paste(AESEV, AESER, sep = concat_sep) COL10 = paste(AETOXGR, AESER_DECODE, sep = concat_sep) ) %>% arrange( COL0, COL1, COL2, !is.na(ASTDYN), ASTDYN, if (include_time) ASTDTM else ASTDT, AEDECOD, AETERM ) lsting <- var_relabel( lsting, COL0 = "Treatment Group", COL1 = "Subject ID", COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep), COL3 = paste( "Onset Dose (unit)", "Day of Last Dose~[super a,b]", sep = concat_sep ), COL4 = paste("Preferred Term", "Reported Term", sep = concat_sep), COL5 = "TE?", COL6 = if (include_time) { paste("Start Date", "Time (Study Day~[super b])", sep = concat_sep) } else { "Start Date (Study Day~[super b])" }, COL7 = if (include_time) { paste("End Date", "Time (Study Day~[super b])", sep = concat_sep) } else { "End Date (Study Day~[super b])" }, # Optional Column: COL8/AEACN COL8 = "Action Taken With Study Treatment", COL9 = "Relationship to Study Treatment~[super c]", # Optional Variable: COL10/AESEV/AETOXGR # COL10 = paste("Severity", "Serious", sep = concat_sep) COL10 = paste("Toxicity Grade", "Serious", sep = concat_sep) ) # Build listing result <- rlistings::as_listing( df = lsting, key_cols = key_cols, disp_cols = disp_cols ) # Add titles and footnotes result <- set_titles(result, tab_titles) # Output listing tt_to_tlgrtf(string_map = string_map, tt = head(result, 100), file = fileid, orientation = "landscape") ``` ```{r result1, echo=FALSE, message=FALSE, warning=FALSE, test = list(result_v1 = "result")} tt_to_flextable_j(head(result,100), tblid, string_map = string_map) ``` [Download RTF file](`r paste0(tolower(tblid), '.rtf')`) ::::