LSFDTH01

Listing of Deaths

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Code

# Program Name:              lsfdth01.R

# Prep environment

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

# Define script level parameters

tblid <- "LSFDTH01"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
key_cols <- c("COL0", "COL1")
disp_cols <- paste0("COL", 0:8)
concat_sep <- " / "
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data

adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y" & DTHFL == "Y")

adexsum <- pharmaverseadamjnj::adexsum %>%
  filter(PARAMCD == "TRTDURM") %>%
  select(STUDYID, USUBJID, AVAL)

adexsum_dig <- tidytlg:::make_precision_data(
  df = adexsum,
  decimal = 4,
  precisionby = "STUDYID",
  precisionon = "AVAL"
) %>%
  rename(c(VALDIGMAX = "decimal"))

adsl_adexsum <- adsl %>%
  inner_join(adexsum, by = c("STUDYID", "USUBJID")) %>%
  left_join(adexsum_dig, by = c("STUDYID" = "STUDYID"))

lsting <- adsl_adexsum %>%
  mutate(
    AGE = explicit_na(as.character(AGE), ""),
    SEX = explicit_na(SEX, ""),
    RACE_DECODE = explicit_na(RACE_DECODE, ""),
    LDOSE = explicit_na(as.character(LDOSE), ""),
    LDOSU = explicit_na(LDOSU, ""),
    DTHCAUS = explicit_na(stringr::str_to_sentence(DTHCAUS), ""),
    DTHTERM = explicit_na(stringr::str_to_sentence(DTHTERM), ""),
    COL0 = explicit_na(.data[[trtvar]], ""),
    COL1 = explicit_na(USUBJID, ""),
    COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
    COL3 = paste(LDOSE, LDOSU),
    COL4 = case_when(
      is.na(AVAL) ~ "",
      VALDIGMAX == 0 & !is.na(AVAL) ~
        tidytlg::roundSAS(AVAL, digits = 0, as_char = TRUE, na_char = NULL),
      VALDIGMAX >= 1 & !is.na(AVAL) ~
        tidytlg::roundSAS(AVAL, digits = 1, as_char = TRUE, na_char = NULL)
    ),
    # Optional Column: COL5/TRTEDT/TRTEDY
    COL5 = ifelse(
      is.na(TRTEDT),
      "",
      paste0(
        toupper(format(TRTEDT, "%d%b%Y")),
        " (",
        TRTEDY,
        ")"
      )
    ),
    # Optional Column: COL6/LDSTODTH
    COL6 = explicit_na(as.character(LDSTODTH), ""),
    COL7 = ifelse(
      is.na(DTHDT),
      "",
      paste0(
        toupper(format(DTHDT, "%d%b%Y")),
        " (",
        DTHDY,
        ")"
      )
    ),
    COL8 = paste(DTHCAUS, DTHTERM, sep = concat_sep)
  ) %>%
  arrange(COL0, COL1)

lsting <- var_relabel(
  lsting,
  COL0 = "Treatment Group",
  COL1 = "Subject ID",
  COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
  COL3 = "Last Dose of Study Treatment",
  COL4 = "Duration of Treatment Months~[super a]",
  # Optional Column: COL5/TRTEDT/TRTEDY
  COL5 = "Date of Last Dose of Study Treatment (Study Day~[super b])",
  # Optional Column: COL6/LDSTODTH
  COL6 = "Days From Last Study Treatment Administration to Death~[super c]",
  COL7 = "Date of Death (Study Day~[super d])",
  COL8 = paste(
    "Primary Cause of Death (Preferred Term",
    "Verbatim",
    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")

LSFDTH01: Listing of Deaths; Safety Analysis Set (Study jjcs - core)
Treatment Group	Subject ID	Age (years) / Sex / Race	Last Dose of Study Treatment	Duration of Treatment Monthsa	Date of Last Dose of Study Treatment (Study Dayb)	Days From Last Study Treatment Administration to Deathc	Date of Death (Study Dayd)	Primary Cause of Death (Preferred Term / Verbatim
Xanomeline Low Dose	01-701-1211	76 / F / Other	20 mg	12.5	12JAN2013 (50)	3	14JAN2013 (61)	Sudden death / Sudden death
Placebo	01-710-1083	89 / F / White	20 mg	11.6	01AUG2013 (50)	2	02AUG2013 (12)	Myocardial infarction / Myocardial infarction

a Duration of treatment is defined as [(date of last dose of [study treatment]– date of first dose of [study treatment]) +1].
b Study day of last dose is defined as date of last dose–[the start of [study treatment]]+1.
c Days from last [study treatment] administration to death=date of death–date of last dose of [study treatment].
d Study day of death is defined as: date of death–[the start of [study treatment]+1.
Note: Cause of death is coded using MedDRA version 26.0.
[lsfdth01.docx][/usr/lib/rstudio-server/bin/quarto/share/rmd/rmd.R] 12JAN2026, 16:09

Download RTF file

--- title: LSFDTH01 subtitle: Listing of Deaths --- ------------------------------------------------------------------------ {{< 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: lsfdth01.R # Prep environment library(envsetup) library(tern) library(dplyr) library(rtables) library(rlistings) library(junco) # Define script level parameters tblid <- "LSFDTH01" fileid <- tblid popfl <- "SAFFL" trtvar <- "TRT01A" key_cols <- c("COL0", "COL1") disp_cols <- paste0("COL", 0:8) concat_sep <- " / " tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map # Process data adsl <- pharmaverseadamjnj::adsl %>% filter(!!rlang::sym(popfl) == "Y" & DTHFL == "Y") adexsum <- pharmaverseadamjnj::adexsum %>% filter(PARAMCD == "TRTDURM") %>% select(STUDYID, USUBJID, AVAL) adexsum_dig <- tidytlg:::make_precision_data( df = adexsum, decimal = 4, precisionby = "STUDYID", precisionon = "AVAL" ) %>% rename(c(VALDIGMAX = "decimal")) adsl_adexsum <- adsl %>% inner_join(adexsum, by = c("STUDYID", "USUBJID")) %>% left_join(adexsum_dig, by = c("STUDYID" = "STUDYID")) lsting <- adsl_adexsum %>% mutate( AGE = explicit_na(as.character(AGE), ""), SEX = explicit_na(SEX, ""), RACE_DECODE = explicit_na(RACE_DECODE, ""), LDOSE = explicit_na(as.character(LDOSE), ""), LDOSU = explicit_na(LDOSU, ""), DTHCAUS = explicit_na(stringr::str_to_sentence(DTHCAUS), ""), DTHTERM = explicit_na(stringr::str_to_sentence(DTHTERM), ""), COL0 = explicit_na(.data[[trtvar]], ""), COL1 = explicit_na(USUBJID, ""), COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep), COL3 = paste(LDOSE, LDOSU), COL4 = case_when( is.na(AVAL) ~ "", VALDIGMAX == 0 & !is.na(AVAL) ~ tidytlg::roundSAS(AVAL, digits = 0, as_char = TRUE, na_char = NULL), VALDIGMAX >= 1 & !is.na(AVAL) ~ tidytlg::roundSAS(AVAL, digits = 1, as_char = TRUE, na_char = NULL) ), # Optional Column: COL5/TRTEDT/TRTEDY COL5 = ifelse( is.na(TRTEDT), "", paste0( toupper(format(TRTEDT, "%d%b%Y")), " (", TRTEDY, ")" ) ), # Optional Column: COL6/LDSTODTH COL6 = explicit_na(as.character(LDSTODTH), ""), COL7 = ifelse( is.na(DTHDT), "", paste0( toupper(format(DTHDT, "%d%b%Y")), " (", DTHDY, ")" ) ), COL8 = paste(DTHCAUS, DTHTERM, sep = concat_sep) ) %>% arrange(COL0, COL1) lsting <- var_relabel( lsting, COL0 = "Treatment Group", COL1 = "Subject ID", COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep), COL3 = "Last Dose of Study Treatment", COL4 = "Duration of Treatment Months~[super a]", # Optional Column: COL5/TRTEDT/TRTEDY COL5 = "Date of Last Dose of Study Treatment (Study Day~[super b])", # Optional Column: COL6/LDSTODTH COL6 = "Days From Last Study Treatment Administration to Death~[super c]", COL7 = "Date of Death (Study Day~[super d])", COL8 = paste( "Primary Cause of Death (Preferred Term", "Verbatim", 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')`) ::::