---
title: LSIEX01
subtitle: Listing of Study Treatment Administration
---
------------------------------------------------------------------------
{{< 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: lsiex01.R
# Prep environment
library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(rlistings)
library(junco)
# Define script level parameters
tblid <- "LSIEX01"
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
# Process data
adex <- pharmaverseadamjnj::adex %>%
filter(!!rlang::sym(popfl) == "Y")
lsting <- adex %>%
mutate(
AGE = explicit_na(as.character(AGE), ""),
SEX = explicit_na(SEX, ""),
RACE_DECODE = explicit_na(RACE_DECODE, ""),
ASTDT = ifelse(
!is.na(ASTDT) & nchar(as.character(ASTDT)) == 10,
toupper(format(ASTDT, "%d%b%Y")),
""
),
ASTTM = ifelse(!is.na(ASTDTM), substr(as.character(ASTDTM), 12, 16), ""),
ASTDYN = ifelse(!is.na(ASTDY), ASTDY, NA),
ASTDY = ifelse(!is.na(ASTDY), ASTDY, ""),
AENDT = ifelse(
!is.na(AENDT) & nchar(as.character(AENDT)) == 10,
toupper(format(AENDT, "%d%b%Y")),
""
),
AENTM = ifelse(!is.na(AENDTM), substr(as.character(AENDTM), 12, 16), ""),
AENDY = ifelse(!is.na(AENDY), AENDY, ""),
AREASOC = explicit_na(AREASOC, ""),
AREASOO = explicit_na(AREASOO, ""),
AADJ = explicit_na(AADJ, ""),
AADJOTH = explicit_na(AADJOTH, ""),
COL0 = explicit_na(.data[[trtvar]], ""),
COL1 = explicit_na(USUBJID, ""),
COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
# Optional Column: COL3/AVISIT
COL3 = explicit_na(AVISIT, ""),
# Optional Column: COL4/ASCHDOSE/ASCHDOSU
COL4 = ifelse(is.na(ASCHDOSE), "", paste(ASCHDOSE, ASCHDOSU)),
COL5 = ifelse(is.na(ADOSE), "", paste(ADOSE, ADOSU)),
# Optional Column: COL6/ADOSFRM/ADOSFRQ/AROUTE
COL6 = paste(
stringr::str_to_sentence(ADOSFRM),
ADOSFRQ,
stringr::str_to_sentence(AROUTE),
sep = concat_sep
),
# Optional Variable: ASTTM
COL7 = case_when(
ASTDT == "" ~ "",
ASTDT != "" & ASTTM != "" & ASTDY != "" ~
paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")"),
ASTDT != "" & ASTTM == "" & ASTDY != "" ~
paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")"),
ASTDT != "" & ASTTM != "" & ASTDY == "" ~
paste0(ASTDT, concat_sep, ASTTM, " (-)"),
ASTDT != "" & ASTTM == "" & ASTDY == "" ~
paste0(ASTDT, concat_sep, "--:--", " (-)"),
),
# Optional Variable: AENTM
COL8 = case_when(
AENDT == "" ~ "",
AENDT != "" & AENTM != "" & AENDY != "" ~
paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")"),
AENDT != "" & AENTM == "" & AENDY != "" ~
paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")"),
AENDT != "" & AENTM != "" & AENDY == "" ~
paste0(AENDT, concat_sep, AENTM, " (-)"),
AENDT != "" & AENTM == "" & AENDY == "" ~
paste0(AENDT, concat_sep, "--:--", " (-)"),
),
# Optional Column: COL9/AREASOC/AREASOO
COL9 = case_when(
toupper(AREASOC) == "OTHER" ~
paste(
stringr::str_to_sentence(AREASOC),
stringr::str_to_sentence(AREASOO),
sep = ": "
),
!is.na(AREASOC) ~ stringr::str_to_sentence(AREASOC),
is.na(AREASOC) ~ ""
),
# Optional Column: COL10/AADJ/AADJOTH
COL10 = case_when(
toupper(AADJ) == "OTHER" ~
paste(
stringr::str_to_sentence(AADJ),
stringr::str_to_sentence(AADJOTH),
sep = ": "
),
!is.na(AADJ) ~ stringr::str_to_sentence(AADJ),
is.na(AADJ) ~ ""
)
) %>%
arrange(COL0, COL1, COL2, !is.na(ASTDYN), ASTDYN, ASTDTM, AVISITN)
lsting <- var_relabel(
lsting,
COL0 = "Treatment Group",
COL1 = "Subject ID",
COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
# Optional Column: COL3/AVISIT
COL3 = "Visit",
# Optional Column: COL4/ASCHDOSE/ASCHDOSU
COL4 = "Prescribed Dose Level (unit)",
COL5 = "Dose (unit)",
# Optional Column: COL6/ADOSFRM/ADOSFRQ/AROUTE
COL6 = paste("Formulation", "Frequency", "Route", sep = concat_sep),
# Optional Variable: ASTTM
COL7 = paste("Start Date", "Time (Study Day~[super a])", sep = concat_sep),
# Optional Variable: AENTM
COL8 = paste("End Date", "Time (Study Day~[super a])", sep = concat_sep),
# Optional Column: COL9/AREASOC/AREASOO
COL9 = "Reason Dose Not Administered, if Applicable",
# Optional Column: COL10/AADJ/AADJOTH
COL10 = "Reason Dose Adjusted, if Applicable"
)
# 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')`)
::::