---
title: LSIEX03
subtitle: Listing of Study Treatment Administration for Infusions
---
------------------------------------------------------------------------
{{< 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: lsiex03.R
# Prep environment
library(envsetup)
library(tern)
library(dplyr)
library(tidyr)
library(rtables)
library(rlistings)
library(junco)
# Define script level parameters
tblid <- "LSIEX03"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
key_cols <- c("COL0", "COL1", "COL2")
disp_cols <- paste0("COL", 0:11)
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(
AACTDU1 = stringr::str_to_sentence(AACTDU1),
AACTDU2 = stringr::str_to_sentence(AACTDU2),
AACTDU3 = stringr::str_to_sentence(AACTDU3),
AACTDU4 = stringr::str_to_sentence(AACTDU4),
AACTDU5 = stringr::str_to_sentence(AACTDU5)
) %>%
unite(
"dact",
AACTDU1,
AACTDU2,
AACTDU3,
AACTDU4,
AACTDU5,
sep = ", ",
na.rm = TRUE,
remove = FALSE
) %>%
mutate(
dact = ifelse(dact == "", NA, dact),
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), ""),
AENDYN = ifelse(!is.na(AENDY), AENDY, NA),
AENDY = ifelse(!is.na(AENDY), AENDY, ""),
preas = case_when(
toupper(AADJP) == "ADVERSE EVENT" ~ stringr::str_to_sentence(AADJP),
toupper(AADJP) == "OTHER" ~
paste0(
stringr::str_to_sentence(AADJP),
": ",
stringr::str_to_sentence(AADJPOTH)
),
is.na(AADJP) & !is.na(AACTPR) ~ "N/A"
),
dreas = case_when(
toupper(AADJ) == "ADVERSE EVENT" ~ stringr::str_to_sentence(AADJ),
toupper(AADJ) == "OTHER" ~
paste0(
stringr::str_to_sentence(AADJ),
": ",
stringr::str_to_sentence(AADJOTH)
),
is.na(AADJ) & !is.na(dact) ~ "N/A"
),
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/ATVINF/ATVINFU
COL6 = ifelse(is.na(ATVINF), "", paste(ATVINF, ATVINFU)),
# Optional Column: COL7/AINFRAT/AINFRAU
COL7 = ifelse(is.na(AINFRAT), "", paste(AINFRAT, AINFRAU)),
COL8 = 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, "--:--", " (-)"),
),
COL9 = 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: COL10/AACTPR/AADJP/AADJPOTH
COL10 = case_when(
!is.na(AACTPR) ~ paste(AACTPR_DECODE, preas, sep = concat_sep),
is.na(AACTPR) & !is.na(preas) ~ paste("", preas, sep = concat_sep),
TRUE ~ ""
),
# Optional Column: COL11/AACTDU1-AACTDU5/AADJ/AADJOTH
COL11 = case_when(
!is.na(dact) ~ paste(dact, dreas, sep = concat_sep),
is.na(dact) & !is.na(dreas) ~ paste("", dreas, sep = concat_sep),
TRUE ~ ""
)
) %>%
arrange(
COL0,
COL1,
COL2,
!is.na(ASTDYN),
ASTDYN,
ASTDTM,
!is.na(AENDYN),
AENDYN,
AENDTM
)
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/ATVINF/ATVINFU
COL6 = "Total Volume Infused (unit)",
# Optional Column: COL7/AINFRAT/AINFRAU
COL7 = "Infusion Rate (unit)",
COL8 = paste("Start Date", "Time (Study Day~[super a])", sep = concat_sep),
COL9 = paste("End Date", "Time (Study Day~[super a])", sep = concat_sep),
# Optional Column: COL10/AACTPR/AADJP/AADJPOTH
COL10 = paste("Action Taken", "Reason Prior to Infusion", sep = concat_sep),
# Optional Column: COL11/AACTDU1-AACTDU5/AADJ/AADJOTH
COL11 = paste("Action Taken", "Reason During Infusion", 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')`)
::::