---
title: LSIEX02
subtitle: Listing of Study Treatment Batch Lot Number
---
------------------------------------------------------------------------
{{< 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: lsiex02.R
# Prep environment
library(envsetup)
library(tern)
library(dplyr)
library(tidyr)
library(rtables)
library(rlistings)
library(junco)
# Define script level parameters
tblid <- "LSIEX02"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
key_cols <- c("COL0", "COL1")
disp_cols <- paste0("COL", 0:6)
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" & ADOSE > 0)
lsting <- adex %>%
mutate(
DAEXPDT = as.Date(DAEXPDTC, format = "%Y-%m-%d"),
DAEXPYR = ifelse(
stringr::str_length(sub("T.*", "", DAEXPDTC)) >= 4 &
substr(sub("T.*", "", DAEXPDTC), 1, 4) != "----",
substr(sub("T.*", "", DAEXPDTC), 1, 4),
NA
),
DAEXPMO = toupper(month.abb[
as.numeric(ifelse(
stringr::str_length(sub("T.*", "", DAEXPDTC)) >= 7 &
substr(sub("T.*", "", DAEXPDTC), 6, 7) != "--",
substr(sub("T.*", "", DAEXPDTC), 6, 7),
NA
))
]),
DAEXPDAY = ifelse(
stringr::str_length(sub("T.*", "", DAEXPDTC)) >= 10 &
substr(sub("T.*", "", DAEXPDTC), 9, 10) != "--",
substr(sub("T.*", "", DAEXPDTC), 9, 10),
NA
),
) %>%
unite(
"DAEXPDTL",
DAEXPDAY,
DAEXPMO,
DAEXPYR,
sep = "",
na.rm = TRUE,
remove = FALSE
) %>%
mutate(
COL0 = explicit_na(.data[[trtvar]], ""),
COL1 = explicit_na(USUBJID, ""),
# Optional Column: COL2/AVISIT
COL2 = explicit_na(AVISIT, ""),
# Optional Column: COL3/ASTDT
COL3 = ifelse(!is.na(ASTDT), paste0(toupper(format(ASTDT, "%d%b%Y"))), ""),
# Optional Column: COL4/ASTDTM
COL4 = ifelse(!is.na(ASTDTM), substr(ASTDTM, 12, 16), ""),
COL5 = explicit_na(EXLOT, ""),
COL6 = explicit_na(DAEXPDTL, "")
) %>%
arrange(
COL0,
COL1,
!is.na(ASTDT),
ASTDT,
!is.na(ASTDTM),
ASTDTM,
AVISITN,
COL2
)
lsting <- var_relabel(
lsting,
COL0 = "Treatment Group",
COL1 = "Subject ID",
# Optional Column: COL2/AVISIT
COL2 = "Visit",
# Optional Column: COL3/ASTDT
# Select appropriate column header label
# COL3 = "Date Dispensed",
COL3 = "Date Administered",
# Optional Column: COL4/ASTDTM
# Select appropriate column header label
# COL4 = "Time Dispensed",
COL4 = "Time Administered",
COL5 = "Batch Lot Number",
COL6 = "Batch Lot Expiration Date"
)
# 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')`)
::::