---
title: LSIDS01
subtitle: Listing of Subjects Who Permanently Discontinued Treatment
---
------------------------------------------------------------------------
{{< 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: lsids01.R
# Prep environment
library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(rlistings)
library(junco)
# Define script level parameters
tblid <- "LSIDS01"
fileid <- tblid
popfl <- "FASFL"
trtvar <- "TRT01P"
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" & !(EOTSTT %in% c("COMPLETED", "ONGOING")))
ds <- pharmaversesdtmjnj::ds %>%
filter(
(DSSCAT %in% c("TREATMENT")) &
DSCAT == "DISPOSITION EVENT" &
DSDECOD != "COMPLETED"
) %>%
select(STUDYID, USUBJID, DSSCAT)
adsl_ds <- adsl %>%
left_join(ds, by = c("STUDYID" = "STUDYID", "USUBJID" = "USUBJID"))
adexsum <- pharmaverseadamjnj::adexsum %>%
filter(PARAMCD == "CUMDOSE") %>%
select(STUDYID, USUBJID, PARAMCD, PARAM, AVAL)
adsl_ds_adexsum <- left_join(
adsl_ds,
adexsum,
by = c(
"STUDYID" = "STUDYID",
"USUBJID" = "USUBJID"
)
)
lsting <- adsl_ds_adexsum %>%
mutate(
AGE = explicit_na(as.character(AGE), ""),
SEX = explicit_na(SEX, ""),
RACE_DECODE = explicit_na(RACE_DECODE, ""),
AVAL = explicit_na(as.character(AVAL), ""),
AVALU = case_when(
!is.na(AVAL) ~
stringr::str_extract(PARAM, "(?<=\\()([^()]*?)(?=\\)[^()]*$)"),
is.na(AVAL) ~
""
),
DCTREAS = explicit_na(DCTREAS, ""),
DCTREASP = explicit_na(DCTREASP, ""),
COL0 = explicit_na(.data[[trtvar]], ""),
COL1 = explicit_na(USUBJID, ""),
COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
# Optional Column: COL3/DSSCAT
COL3 = explicit_na(stringr::str_to_sentence(DSSCAT), ""),
# Optional Column: COL4/LTVISIT
COL4 = explicit_na(LTVISIT, ""),
COL5 = explicit_na(as.character(TRTEDY), ""),
# Optional Column: COL6/CUMDOSE/CUMDOSU
COL6 = paste0(AVAL, " ", AVALU),
COL7 = ifelse(
is.na(DCTDT),
"",
toupper(format(as.Date(DCTDT), format = "%d%b%Y"))
),
COL8 = case_when(
DCTREAS == "OTHER" ~
paste0(DCTREAS, " (", stringr::str_to_sentence(DCTREASP), ")"),
DCTREAS != "OTHER" ~
DCTREAS
)
) %>%
arrange(COL0, COL1, COL2, COL3)
lsting <- var_relabel(
lsting,
COL0 = "Treatment Group",
COL1 = "Subject ID",
COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
# Optional Column: COL3/DSSCAT
COL3 = "Study Agent Discontinued",
# Optional Column: COL4/LTVISIT
COL4 = "Last Visit~[super a]",
COL5 = "Study Day~[super b] of Last Study Agent Administered",
# Optional Column: COL6/CUMDOSE/CUMDOSU
COL6 = "Total Dose (unit)~[super c]",
COL7 = "Date of Discontinuation",
COL8 = "Primary Reason for Discontinuation"
)
# 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')`)
::::