---
title: LSFLAB01
subtitle: Listing of Subjects With Criteria Laboratory Values
---
------------------------------------------------------------------------
{{< 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: lsflab01.R
# Prep environment
library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(rlistings)
library(junco)
# Define script level parameters
tblid <- "LSFLAB01"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
key_cols <- c("COL0", "COL1", "COL2", "COL3")
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
adlb <- pharmaverseadamjnj::adlb %>%
filter(!!rlang::sym(popfl) == "Y" & is.na(DTYPE))
adlb <- adlb[1:1000, ] # make it manageable
adlb_crit <- adlb %>%
# Update filter criteria as needed for your study
# MCRIT1ML/MCRI2ML or ATOXGRN will be used
filter(
((!is.na(MCRIT1ML) & as.numeric(substr(MCRIT1ML, 7, 8)) >= 2) |
(!is.na(MCRIT2ML) & as.numeric(substr(MCRIT2ML, 7, 8)) >= 2))
) %>%
# filter(ATOXGRN >= 3) %>%
select(STUDYID, USUBJID, PARAMCD) %>%
distinct()
adlb_dig <- tidytlg:::make_precision_data(
df = adlb,
decimal = 4,
precisionby = "PARAMCD",
precisionon = "AVAL"
) %>%
rename(c(VALDIGMAX = "decimal"))
adlb_list <- adlb_crit %>%
inner_join(
adlb,
by = c(
"STUDYID" = "STUDYID",
"USUBJID" = "USUBJID",
"PARAMCD" = "PARAMCD"
)
) %>%
inner_join(adlb_dig, by = c("PARAMCD" = "PARAMCD"))
lsting <- adlb_list %>%
mutate(
AGE = explicit_na(as.character(AGE), ""),
SEX = explicit_na(SEX, ""),
RACE_DECODE = explicit_na(RACE_DECODE, ""),
ADT = ifelse(
nchar(as.character(ADT)) == 10,
toupper(format(ADT, "%d%b%Y")),
"---------"
),
ATM = ifelse(!is.na(ADTM), substr(as.character(ADTM), 12, 16), "--:--"),
ADYN = ifelse(!is.na(ADY), ADY, NA),
ADY = ifelse(!is.na(ADY), ADY, "--"),
VAL_RES = case_when(
is.na(VALDIGMAX) & !is.na(AVAL) ~
tidytlg::roundSAS(AVAL, digits = 0, as_char = TRUE, na_char = NULL),
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),
VALDIGMAX == 2 & !is.na(AVAL) ~
tidytlg::roundSAS(AVAL, digits = 2, as_char = TRUE, na_char = NULL),
VALDIGMAX == 3 & !is.na(AVAL) ~
tidytlg::roundSAS(AVAL, digits = 3, as_char = TRUE, na_char = NULL),
VALDIGMAX >= 4 & !is.na(AVAL) ~
tidytlg::roundSAS(AVAL, digits = 4, as_char = TRUE, na_char = NULL),
!is.na(AVALC) ~ AVALC
),
VAL_HL = case_when(
!is.na(ANRIND) ~ substr(ANRIND, 1, 1),
.default = NA
),
VAL_CS = case_when(
LBCLSIG == "Y" ~ "CS",
LBCLSIG == "N" ~ "NCS",
.default = NA
),
VAL = case_when(
!is.na(VAL_RES) & !is.na(VAL_HL) & !is.na(VAL_CS) ~ paste(
VAL_RES,
VAL_HL,
VAL_CS,
sep = " "
),
!is.na(VAL_RES) & !is.na(VAL_HL) & is.na(VAL_CS) ~ paste(
VAL_RES,
VAL_HL,
sep = " "
),
!is.na(VAL_RES) & is.na(VAL_HL) & !is.na(VAL_CS) ~ paste(
VAL_RES,
VAL_CS,
sep = " "
),
!is.na(VAL_RES) & is.na(VAL_HL) & is.na(VAL_CS) ~ VAL_RES,
.default = NA
),
ANRIND = substr(ANRIND, 1, 1),
MCRIT1ML = ifelse(
MCRIT1ML != "Level 0",
paste0(
"L",
substr(MCRIT1ML, 7, 8),
substr(
MCRIT1ML,
9,
nchar(as.character(MCRIT1ML))
)
),
NA
),
MCRIT2ML = ifelse(
MCRIT2ML != "Level 0",
paste0(
"L",
substr(MCRIT2ML, 7, 8),
substr(
MCRIT2ML,
9,
nchar(as.character(MCRIT2ML))
)
),
NA
),
CRIT = case_when(
is.na(MCRIT1ML) & is.na(MCRIT2ML) ~ "",
!is.na(MCRIT1ML) ~ MCRIT1ML,
!is.na(MCRIT2ML) ~ MCRIT2ML,
),
# CRIT = ifelse(!is.na(ATOXGR), as.character(ATOXGR), ""),
REFRL = case_when(
is.na(LBSTNRLO) ~ as.character(ANRLO),
!is.na(LBSTNRLQ) & !is.na(LBSTNRLO) ~ paste0(
LBSTNRLQ,
as.character(LBSTNRLO)
),
is.na(LBSTNRLQ) & !is.na(LBSTNRLO) ~ as.character(LBSTNRLO),
.default = "NA"
),
REFRH = case_when(
is.na(LBSTNRHI) ~ as.character(ANRHI),
!is.na(LBSTNRHQ) & !is.na(LBSTNRHI) ~ paste0(
LBSTNRHQ,
as.character(LBSTNRHI)
),
is.na(LBSTNRHQ) & !is.na(LBSTNRHI) ~ as.character(LBSTNRHI),
.default = "NA"
),
REFR = case_when(
!is.na(REFRL) & !is.na(REFRH) ~ paste(REFRL, REFRH, sep = " - "),
!is.na(REFRL) & is.na(REFRH) ~ paste(REFRL, " ", sep = "- "),
is.na(REFRL) & !is.na(REFRH) ~ paste(" ", REFRH, sep = "- ")
),
COL0 = explicit_na(.data[[trtvar]], ""),
COL1 = explicit_na(USUBJID, ""),
COL2 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
COL3 = explicit_na(PARAM, ""),
# Optional Variable: ATM
COL4 = paste0(ADT, concat_sep, ATM, " (", ADY, ")", sep = ""),
COL5 = explicit_na(AVISIT, ""),
# Optional Column: COL6/ATPT
COL6 = explicit_na(ATPT, ""),
COL7 = explicit_na(VAL, ""),
# Optional Variable: COL8/MCRIT1ML/MCRIT2ML/ATOXGR
COL8 = explicit_na(CRIT, ""),
COL9 = case_when(
is.na(CHG) ~ "",
is.na(VALDIGMAX) & !is.na(AVAL) & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 0, as_char = TRUE, na_char = NULL),
VALDIGMAX == 0 & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 0, as_char = TRUE, na_char = NULL),
VALDIGMAX == 1 & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 1, as_char = TRUE, na_char = NULL),
VALDIGMAX == 2 & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 2, as_char = TRUE, na_char = NULL),
VALDIGMAX == 3 & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 3, as_char = TRUE, na_char = NULL),
VALDIGMAX >= 4 & !is.na(CHG) ~
tidytlg::roundSAS(CHG, digits = 4, as_char = TRUE, na_char = NULL)
),
# Optional Column: COL10/ANRLO/ANRHI
COL10 = explicit_na(REFR, ""),
) %>%
arrange(COL0, COL1, COL2, COL3, COL4, !is.na(ADYN), ADYN, ADTM)
lsting <- var_relabel(
lsting,
COL0 = "Treatment Group",
COL1 = "Subject ID",
COL2 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
COL3 = "Laboratory Test (unit)",
# Optional Variable: ATM
COL4 = paste(
"Assessment Date",
"Time (Study Day~[super a])",
sep = concat_sep
),
COL5 = "Visit",
# Optional Column: COL6/ATPT
COL6 = "Time Point",
COL7 = "Result",
# Optional Variable: COL8/MCRIT1ML/MCRIT2ML/ATOXGR
COL8 = "FDA Threshold Level",
# COL9 = "Toxicity Grade",
COL9 = "Change From Baseline",
# Optional Column: COL10/ANRLO/ANRHI
COL10 = "Reference Range"
)
# 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')`)
::::