From 9955da6cae2b790b5c66f7a8cb7b53b0b8a3fd2d Mon Sep 17 00:00:00 2001
From: "Alcaraz, Josue {TBB~SOUTH SAN FRANCISCO}" <alcaraz.josue@gene.com>
Date: Tue, 16 Jul 2024 17:14:50 +0200
Subject: [PATCH 1/4] Added DM parameter and merge when SITEID variable exists
---
R/check_lb_lbstresn_missing.R | 68 ++++++++++++++++++++++++-----------
R/check_lb_lbstresu.R | 47 ++++++++++++++++++------
2 files changed, 84 insertions(+), 31 deletions(-)
diff --git a/R/check_lb_lbstresn_missing.R b/R/check_lb_lbstresn_missing.R
index bb500cf1..cd0f2510 100755
--- a/R/check_lb_lbstresn_missing.R
+++ b/R/check_lb_lbstresn_missing.R
@@ -1,10 +1,12 @@
#' @title Check missing standard lab values (LBSTRESN/LBSTRESC)
#'
#' @description This check looks for missing standardized finding (LBSTRESN/LBSTRESC)
-#' when original finding (LBORRES) is not missing
+#' when original finding (LBORRES) is not missing. Merges with DM dataset
+#' when DM$SITEID is present
#'
#' @param LB Lab SDTM dataset with variables USUBJID, LBTESTCD, LBDTC, LBORRES,
#' LBORRESU, LBSTRESN, LBSTRESC, VISIT (optional), LBSPID (optional)
+#' @param DM Demographics SDTM with variables USUBJID, SITEID
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
@@ -33,55 +35,79 @@
#' LBSTRESN = c(5,6,NA),
#' stringsAsFactors=FALSE
#' )
+#'
+#' DM <- data.frame(
+#' USUBJID = c("Patient 1","Patient 2","Patient 3"),
+#' SITEID = c("123","124","125"),
+#' stringsAsFactors=FALSE
+#' )
+#'
+#' DM2 <- data.frame(
+#' USUBJID = c("Patient 1","Patient 2","Patient 3"),
+#' stringsAsFactors=FALSE
+#' )
#'
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
#'
#' LB$LBSTRESC[3] = ""
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
+#'
+#' LB$LBSTRESC[3] = ""
+#' check_lb_lbstresn_missing(LB, DM2)
#'
#' LB$LBSTRESC[1] = ""
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
#'
#' LB$VISIT = "SCREENING"
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
#'
#' LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
#' check_lb_lbstresn_missing(LB,preproc=roche_derive_rave_row)
#'
#' LB$LBSTRESN = NULL
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
#'
#' LB$LBSTRESC = NULL
-#' check_lb_lbstresn_missing(LB)
+#' check_lb_lbstresn_missing(LB, DM)
#'
-check_lb_lbstresn_missing <- function(LB,preproc=identity,...){
-
+check_lb_lbstresn_missing <- function(LB, DM,preproc=identity,...){
+
if(LB %lacks_any% c("USUBJID", "LBTESTCD", "LBDTC", "LBORRES", "LBORRESU", "LBSTRESN", "LBSTRESC")){
-
+
fail(lacks_msg(LB, c("USUBJID", "LBTESTCD", "LBDTC", "LBORRES", "LBORRESU", "LBSTRESN", "LBSTRESC")))
-
+
}else{
-
+
+ # Subset DM to fewer variables
+ DM <- DM %>%
+ select(any_of(c("USUBJID", "SITEID")))
+
+ # Merge DM to LB if SITEID exists
+ if("SITEID" %in% names(DM)){
+ LB <- left_join(LB, DM, by="USUBJID")
+ }
+
#Apply company specific preprocessing function
LB = preproc(LB,...)
-
+
# Subset LB to fewer variables
LB <- LB %>%
- select(any_of(c("USUBJID", "LBTESTCD", "LBDTC", "LBORRES", "LBORRESU", "LBSTRESN", "LBSTRESC","RAVE","VISIT")))
-
+ select(any_of(c("USUBJID", "LBTESTCD", "LBDTC", "LBORRES", "LBORRESU",
+ "LBSTRESN", "LBSTRESC", "RAVE", "VISIT", "SITEID" )))
+
# Subset to LBORRES populated but LBSTRESN not
mydf <- subset(LB, !is_sas_na(LB$LBORRES) & is_sas_na(LB$LBSTRESN) & is_sas_na(LB$LBSTRESC))
-
+
if (nrow(mydf)==0){
pass()
}
else if (nrow(mydf)>0) {
- fail(paste0(length(unique(mydf$USUBJID)),
- " unique patient(s) with ",
- nrow(mydf),
- " lab record(s) with result reported without standard value. "),
- mydf)
+ fail(paste0(length(unique(mydf$USUBJID)),
+ " unique patient(s) with ",
+ nrow(mydf),
+ " lab record(s) with result reported without standard value. "),
+ mydf)
}
}
}
diff --git a/R/check_lb_lbstresu.R b/R/check_lb_lbstresu.R
index c1e5357f..f0ebf2a7 100755
--- a/R/check_lb_lbstresu.R
+++ b/R/check_lb_lbstresu.R
@@ -3,11 +3,12 @@
#' @description This check identifies records where original lab values (LBORRES)
#' exist but standard lab units (LBSTRESU) are not populated, excluding
#' qualitative results (LBMETHOD) and excluding records when LBTESTCD in
-#' ("PH" "SPGRAV")
+#' ("PH" "SPGRAV"). Merges with DM dataset when DM$SITEID is present
#'
#' @param LB Lab SDTM dataset with variables USUBJID, LBSTRESC, LBSTRESN,
#' LBORRES, LBSTRESU, LBTESTCD, LBDTC, LBMETHOD (optional),
#' LBSPID (optional), and VISIT (optional)
+#' @param DM Demographics SDTM with variables USUBJID, SITEID
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
@@ -34,28 +35,43 @@
#' stringsAsFactors=FALSE
#' )
#'
-#' check_lb_lbstresu(LB)
+#' DM <- data.frame(
+#' USUBJID = 1:10,
+#' SITEID = 111:120,
+#' stringsAsFactors=FALSE
+#' )
+#'
+#' DM2 <- data.frame(
+#' USUBJID = 1:10,
+#' stringsAsFactors=FALSE
+#' )
+#'
+#'
+#' check_lb_lbstresu(LB, DM)
#'
#' LB$LBSTRESU[1]=""
-#' check_lb_lbstresu(LB)
+#' check_lb_lbstresu(LB, DM)
+#'
+#' LB$LBSTRESU[1]=""
+#' check_lb_lbstresu(LB, DM2)
#'
#' LB$LBSTRESU[2]="NA"
-#' check_lb_lbstresu(LB)
+#' check_lb_lbstresu(LB, DM)
#'
#' LB$LBSTRESU[3]=NA
-#' check_lb_lbstresu(LB)
+#' check_lb_lbstresu(LB, DM)
#'
#' LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
-#' check_lb_lbstresu(LB,preproc=roche_derive_rave_row)
+#' check_lb_lbstresu(LB, DM, preproc=roche_derive_rave_row)
#'
#' LB$VISIT= "SCREENING"
-#' check_lb_lbstresu(LB)
+#' check_lb_lbstresu(LB, DM)
#'
#' LB$LBSTRESU=NULL
-#' check_lb_lbstresu(LB)
+#' check_lb_lbstresu(LB, DM)
#'
-check_lb_lbstresu <- function(LB,preproc=identity,...){
+check_lb_lbstresu <- function(LB, DM, preproc=identity,...){
###Check that required variables exist and return a message if they don't.
if(LB %lacks_any% c("USUBJID", "LBSTRESC", "LBSTRESN", "LBSTRESU", "LBORRES",
@@ -64,6 +80,16 @@ check_lb_lbstresu <- function(LB,preproc=identity,...){
"LBTESTCD", "LBDTC")))
} else{
+ # Subset DM to fewer variables
+ DM <- DM %>%
+ select(any_of(c("USUBJID", "SITEID")))
+
+ # Merge DM to LB if SITEID exists
+ if("SITEID" %in% names(DM)){
+ LB <- left_join(LB, DM, by="USUBJID")
+ }
+
+
#Apply company specific preprocessing function
LB = preproc(LB,...)
@@ -82,7 +108,8 @@ check_lb_lbstresu <- function(LB,preproc=identity,...){
# Subset LB to fewer variables
df <- LB %>%
- select(any_of(c('USUBJID','LBTESTCD','LBORRES','LBSTRESU','LBSTRESC','LBDTC','RAVE','VISIT')))
+ select(any_of(c('USUBJID','LBTESTCD','LBORRES','LBSTRESU','LBSTRESC','LBDTC',
+ 'RAVE','VISIT', 'SITEID')))
### Exclude particular labs known to be unitless
df <- df %>%
From 3a8c97cb5c65225ca5effc8505cf86a42ea184a9 Mon Sep 17 00:00:00 2001
From: AlcJ123 <AlcJ123@users.noreply.github.com>
Date: Tue, 16 Jul 2024 15:22:25 +0000
Subject: [PATCH 2/4] Update documentation
---
man/check_lb_lbstresn_missing.Rd | 33 ++++++++++++++++++++++--------
man/check_lb_lbstresu.Rd | 35 ++++++++++++++++++++++++--------
2 files changed, 51 insertions(+), 17 deletions(-)
diff --git a/man/check_lb_lbstresn_missing.Rd b/man/check_lb_lbstresn_missing.Rd
index d3a0e66a..fd0bb46f 100644
--- a/man/check_lb_lbstresn_missing.Rd
+++ b/man/check_lb_lbstresn_missing.Rd
@@ -4,12 +4,14 @@
\alias{check_lb_lbstresn_missing}
\title{Check missing standard lab values (LBSTRESN/LBSTRESC)}
\usage{
-check_lb_lbstresn_missing(LB, preproc = identity, ...)
+check_lb_lbstresn_missing(LB, DM, preproc = identity, ...)
}
\arguments{
\item{LB}{Lab SDTM dataset with variables USUBJID, LBTESTCD, LBDTC, LBORRES,
LBORRESU, LBSTRESN, LBSTRESC, VISIT (optional), LBSPID (optional)}
+\item{DM}{Demographics SDTM with variables USUBJID, SITEID}
+
\item{preproc}{An optional company specific preprocessing script}
\item{...}{Other arguments passed to methods}
@@ -20,7 +22,8 @@ test failed
}
\description{
This check looks for missing standardized finding (LBSTRESN/LBSTRESC)
-when original finding (LBORRES) is not missing
+when original finding (LBORRES) is not missing. Merges with DM dataset
+when DM$SITEID is present
}
\examples{
@@ -35,26 +38,40 @@ LB <- data.frame(
LBSTRESN = c(5,6,NA),
stringsAsFactors=FALSE
)
+
+ DM <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ SITEID = c("123","124","125"),
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ stringsAsFactors=FALSE
+ )
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM)
+
+LB$LBSTRESC[3] = ""
+check_lb_lbstresn_missing(LB, DM)
LB$LBSTRESC[3] = ""
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM2)
LB$LBSTRESC[1] = ""
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM)
LB$VISIT = "SCREENING"
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM)
LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
check_lb_lbstresn_missing(LB,preproc=roche_derive_rave_row)
LB$LBSTRESN = NULL
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM)
LB$LBSTRESC = NULL
-check_lb_lbstresn_missing(LB)
+check_lb_lbstresn_missing(LB, DM)
}
\author{
diff --git a/man/check_lb_lbstresu.Rd b/man/check_lb_lbstresu.Rd
index 54f224b9..ecee4a4e 100644
--- a/man/check_lb_lbstresu.Rd
+++ b/man/check_lb_lbstresu.Rd
@@ -4,13 +4,15 @@
\alias{check_lb_lbstresu}
\title{Check for missing lab units (LBSTRESU)}
\usage{
-check_lb_lbstresu(LB, preproc = identity, ...)
+check_lb_lbstresu(LB, DM, preproc = identity, ...)
}
\arguments{
\item{LB}{Lab SDTM dataset with variables USUBJID, LBSTRESC, LBSTRESN,
LBORRES, LBSTRESU, LBTESTCD, LBDTC, LBMETHOD (optional),
LBSPID (optional), and VISIT (optional)}
+\item{DM}{Demographics SDTM with variables USUBJID, SITEID}
+
\item{preproc}{An optional company specific preprocessing script}
\item{...}{Other arguments passed to methods}
@@ -23,7 +25,7 @@ test failed
This check identifies records where original lab values (LBORRES)
exist but standard lab units (LBSTRESU) are not populated, excluding
qualitative results (LBMETHOD) and excluding records when LBTESTCD in
-("PH" "SPGRAV")
+("PH" "SPGRAV"). Merges with DM dataset when DM$SITEID is present
}
\examples{
@@ -38,25 +40,40 @@ LBDTC = 1:10,
stringsAsFactors=FALSE
)
-check_lb_lbstresu(LB)
+ DM <- data.frame(
+ USUBJID = 1:10,
+ SITEID = 111:120,
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+
+check_lb_lbstresu(LB, DM)
+
+LB$LBSTRESU[1]=""
+check_lb_lbstresu(LB, DM)
LB$LBSTRESU[1]=""
-check_lb_lbstresu(LB)
+check_lb_lbstresu(LB, DM2)
LB$LBSTRESU[2]="NA"
-check_lb_lbstresu(LB)
+check_lb_lbstresu(LB, DM)
LB$LBSTRESU[3]=NA
-check_lb_lbstresu(LB)
+check_lb_lbstresu(LB, DM)
LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
-check_lb_lbstresu(LB,preproc=roche_derive_rave_row)
+check_lb_lbstresu(LB, DM, preproc=roche_derive_rave_row)
LB$VISIT= "SCREENING"
-check_lb_lbstresu(LB)
+check_lb_lbstresu(LB, DM)
LB$LBSTRESU=NULL
-check_lb_lbstresu(LB)
+check_lb_lbstresu(LB, DM)
}
\author{
From cdc46a466d3179402043ad63aef52cb176b17847 Mon Sep 17 00:00:00 2001
From: "Alcaraz, Josue {TBB~SOUTH SAN FRANCISCO}" <alcaraz.josue@gene.com>
Date: Thu, 25 Jul 2024 03:31:03 +0200
Subject: [PATCH 3/4] Default to DM=NULL, added logic for if !is.null(DM) for
both functions. Created new unit checks for when DM has and does not have
siteid variable.
---
R/check_lb_lbstresn_missing.R | 30 +--
R/check_lb_lbstresu.R | 36 +--
.../testthat/test-check_lb_lbstresn_missing.R | 196 ++++++++++++++--
tests/testthat/test-check_lb_lbstresu.R | 215 +++++++++++++++---
4 files changed, 406 insertions(+), 71 deletions(-)
diff --git a/R/check_lb_lbstresn_missing.R b/R/check_lb_lbstresn_missing.R
index cd0f2510..e2bf6461 100755
--- a/R/check_lb_lbstresn_missing.R
+++ b/R/check_lb_lbstresn_missing.R
@@ -6,7 +6,7 @@
#'
#' @param LB Lab SDTM dataset with variables USUBJID, LBTESTCD, LBDTC, LBORRES,
#' LBORRESU, LBSTRESN, LBSTRESC, VISIT (optional), LBSPID (optional)
-#' @param DM Demographics SDTM with variables USUBJID, SITEID
+#' @param DM Demographics SDTM with variables USUBJID, SITEID. Set to NULL.
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
@@ -47,31 +47,32 @@
#' stringsAsFactors=FALSE
#' )
#'
-#' check_lb_lbstresn_missing(LB, DM)
+#' check_lb_lbstresn_missing(LB)
#'
#' LB$LBSTRESC[3] = ""
+#' check_lb_lbstresn_missing(LB)
+#'
#' check_lb_lbstresn_missing(LB, DM)
#'
-#' LB$LBSTRESC[3] = ""
#' check_lb_lbstresn_missing(LB, DM2)
#'
#' LB$LBSTRESC[1] = ""
-#' check_lb_lbstresn_missing(LB, DM)
+#' check_lb_lbstresn_missing(LB)
#'
#' LB$VISIT = "SCREENING"
-#' check_lb_lbstresn_missing(LB, DM)
+#' check_lb_lbstresn_missing(LB)
#'
#' LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
#' check_lb_lbstresn_missing(LB,preproc=roche_derive_rave_row)
#'
#' LB$LBSTRESN = NULL
-#' check_lb_lbstresn_missing(LB, DM)
+#' check_lb_lbstresn_missing(LB)
#'
#' LB$LBSTRESC = NULL
-#' check_lb_lbstresn_missing(LB, DM)
+#' check_lb_lbstresn_missing(LB)
#'
-check_lb_lbstresn_missing <- function(LB, DM,preproc=identity,...){
+check_lb_lbstresn_missing <- function(LB, DM = NULL,preproc=identity,...){
if(LB %lacks_any% c("USUBJID", "LBTESTCD", "LBDTC", "LBORRES", "LBORRESU", "LBSTRESN", "LBSTRESC")){
@@ -79,12 +80,12 @@ check_lb_lbstresn_missing <- function(LB, DM,preproc=identity,...){
}else{
- # Subset DM to fewer variables
- DM <- DM %>%
- select(any_of(c("USUBJID", "SITEID")))
-
- # Merge DM to LB if SITEID exists
- if("SITEID" %in% names(DM)){
+ # If DM is present, merge by USUBJID
+ if(!is.null(DM) & "SITEID" %in% names(DM)){
+
+ DM <- DM %>%
+ select(any_of(c("USUBJID", "SITEID")))
+
LB <- left_join(LB, DM, by="USUBJID")
}
@@ -111,3 +112,4 @@ check_lb_lbstresn_missing <- function(LB, DM,preproc=identity,...){
}
}
}
+
diff --git a/R/check_lb_lbstresu.R b/R/check_lb_lbstresu.R
index f0ebf2a7..f17c04b9 100755
--- a/R/check_lb_lbstresu.R
+++ b/R/check_lb_lbstresu.R
@@ -8,7 +8,7 @@
#' @param LB Lab SDTM dataset with variables USUBJID, LBSTRESC, LBSTRESN,
#' LBORRES, LBSTRESU, LBTESTCD, LBDTC, LBMETHOD (optional),
#' LBSPID (optional), and VISIT (optional)
-#' @param DM Demographics SDTM with variables USUBJID, SITEID
+#' @param DM Demographics SDTM with variables USUBJID, SITEID. Set to NULL.
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
@@ -47,31 +47,35 @@
#' )
#'
#'
-#' check_lb_lbstresu(LB, DM)
+#' check_lb_lbstresu(LB)
#'
#' LB$LBSTRESU[1]=""
+#' check_lb_lbstresu(LB)
+#'
+#' check_lb_lbstresu(LB, DM2)
+#'
#' check_lb_lbstresu(LB, DM)
#'
#' LB$LBSTRESU[1]=""
-#' check_lb_lbstresu(LB, DM2)
+#' check_lb_lbstresu(LB)
#'
#' LB$LBSTRESU[2]="NA"
-#' check_lb_lbstresu(LB, DM)
+#' check_lb_lbstresu(LB)
#'
#' LB$LBSTRESU[3]=NA
-#' check_lb_lbstresu(LB, DM)
+#' check_lb_lbstresu(LB)
#'
#' LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
#' check_lb_lbstresu(LB, DM, preproc=roche_derive_rave_row)
#'
#' LB$VISIT= "SCREENING"
-#' check_lb_lbstresu(LB, DM)
+#' check_lb_lbstresu(LB)
#'
#' LB$LBSTRESU=NULL
-#' check_lb_lbstresu(LB, DM)
+#' check_lb_lbstresu(LB)
#'
-check_lb_lbstresu <- function(LB, DM, preproc=identity,...){
+check_lb_lbstresu <- function(LB, DM = NULL, preproc=identity,...){
###Check that required variables exist and return a message if they don't.
if(LB %lacks_any% c("USUBJID", "LBSTRESC", "LBSTRESN", "LBSTRESU", "LBORRES",
@@ -80,16 +84,15 @@ check_lb_lbstresu <- function(LB, DM, preproc=identity,...){
"LBTESTCD", "LBDTC")))
} else{
- # Subset DM to fewer variables
- DM <- DM %>%
- select(any_of(c("USUBJID", "SITEID")))
-
- # Merge DM to LB if SITEID exists
- if("SITEID" %in% names(DM)){
+ # If DM is present, merge by USUBJID
+ if(!is.null(DM) & "SITEID" %in% names(DM)){
+
+ DM <- DM %>%
+ select(any_of(c("USUBJID", "SITEID")))
+
LB <- left_join(LB, DM, by="USUBJID")
}
-
#Apply company specific preprocessing function
LB = preproc(LB,...)
@@ -133,4 +136,5 @@ check_lb_lbstresu <- function(LB, DM, preproc=identity,...){
}
-}
\ No newline at end of file
+}
+
diff --git a/tests/testthat/test-check_lb_lbstresn_missing.R b/tests/testthat/test-check_lb_lbstresn_missing.R
index d0ea716d..28faba12 100644
--- a/tests/testthat/test-check_lb_lbstresn_missing.R
+++ b/tests/testthat/test-check_lb_lbstresn_missing.R
@@ -1,20 +1,22 @@
test_that("Function returns true when no errors are present", {
LB <- data.frame(
- USUBJID = c("Patient 1","Patient 2","Patient 3"),
- LBTEST = "Test A",
- LBTESTCD = "TA",
- LBDTC = "2017-01-01",
- LBORRES = c("5","6","7"),
- LBSTRESC = c("5","6","7"),
- LBORRESU = rep("mg",3),
- LBSTRESN = c(5,6,NA),
- stringsAsFactors=FALSE
- )
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
expect_true(check_lb_lbstresn_missing(LB))
})
+
+
test_that("Function returns false when errors are present", {
LB <- data.frame(
@@ -39,10 +41,87 @@ test_that("Function returns false when errors are present", {
+test_that("Function returns false when expected column not present", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESC=NULL
+ LB$LBSTRESN=NULL
+
+ expect_false(check_lb_lbstresn_missing(LB))
+
+})
-test_that("Function returns false when expected column not present", {
+test_that("Function returns true when no errors are present, DM is present with SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ DM <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ SITEID = c("123","124","125"),
+ stringsAsFactors=FALSE
+ )
+
+ expect_true(check_lb_lbstresn_missing(LB, DM))
+})
+
+
+
+test_that("Function returns false when errors are present, DM is present with SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ DM <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ SITEID = c("123","124","125"),
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESC[3] = ""
+ LB$LBSTRESC[1] = ""
+ LB$VISIT = "SCREENING"
+
+
+
+ expect_false(check_lb_lbstresn_missing(LB, DM))
+
+})
+
+
+test_that("Function returns false when expected column not present, DM is present with SITEID variable", {
+
LB <- data.frame(
USUBJID = c("Patient 1","Patient 2","Patient 3"),
LBTEST = "Test A",
@@ -55,10 +134,99 @@ test_that("Function returns false when expected column not present", {
stringsAsFactors=FALSE
)
+ DM <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ SITEID = c("123","124","125"),
+ stringsAsFactors=FALSE
+ )
+
LB$LBSTRESC=NULL
LB$LBSTRESN=NULL
- expect_false(check_lb_lbstresn_missing(LB))
-
- })
+ expect_false(check_lb_lbstresn_missing(LB, DM))
+
+})
+
+
+
+test_that("Function returns true when no errors are present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ stringsAsFactors=FALSE
+ )
+
+ expect_true(check_lb_lbstresn_missing(LB, DM2))
+})
+
+
+
+test_that("Function returns false when errors are present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESC[3] = ""
+ LB$LBSTRESC[1] = ""
+ LB$VISIT = "SCREENING"
+
+ expect_false(check_lb_lbstresn_missing(LB, DM2))
+
+})
+
+
+
+test_that("Function returns false when expected column not present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ LBTEST = "Test A",
+ LBTESTCD = "TA",
+ LBDTC = "2017-01-01",
+ LBORRES = c("5","6","7"),
+ LBSTRESC = c("5","6","7"),
+ LBORRESU = rep("mg",3),
+ LBSTRESN = c(5,6,NA),
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = c("Patient 1","Patient 2","Patient 3"),
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESC=NULL
+ LB$LBSTRESN=NULL
+
+ expect_false(check_lb_lbstresn_missing(LB,DM2))
+
+})
+
+
diff --git a/tests/testthat/test-check_lb_lbstresu.R b/tests/testthat/test-check_lb_lbstresu.R
index 1c8564f2..be835fad 100644
--- a/tests/testthat/test-check_lb_lbstresu.R
+++ b/tests/testthat/test-check_lb_lbstresu.R
@@ -1,20 +1,22 @@
test_that("Function returns true when no errors are present", {
LB <- data.frame(
- USUBJID = 1:10,
- LBSTRESC = "5",
- LBSTRESN = 1:10,
- LBORRES = "5",
- LBSTRESU = "g/L",
- LBTESTCD = "ALB",
- LBDTC = 1:10,
- stringsAsFactors=FALSE
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
)
expect_true(check_lb_lbstresu(LB))
})
+
+
test_that("Function returns false when errors are present", {
LB <- data.frame(
@@ -28,9 +30,9 @@ test_that("Function returns false when errors are present", {
stringsAsFactors=FALSE
)
- LB$LBSTRESU[1]=""
- LB$LBSTRESU[2]="NA"
- LB$LBSTRESU[3]=NA
+ LB$LBSTRESU[1]=""
+ LB$LBSTRESU[2]="NA"
+ LB$LBSTRESU[3]=NA
expect_false(check_lb_lbstresu(LB))
@@ -39,21 +41,180 @@ test_that("Function returns false when errors are present", {
test_that("Function returns false when expected column not present", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESU=NULL
+
+ expect_false(check_lb_lbstresu(LB))
+
+})
+
+
+
+test_that("Function returns true when no errors are present, DM is present with SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ DM <- data.frame(
+ USUBJID = 1:10,
+ SITEID = 111:120,
+ stringsAsFactors=FALSE
+ )
+
+ expect_true(check_lb_lbstresu(LB, DM))
+})
+
+
+
+test_that("Function returns false when errors are present, DM is present with SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ DM <- data.frame(
+ USUBJID = 1:10,
+ SITEID = 111:120,
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESU[1]=""
+ LB$LBSTRESU[2]="NA"
+ LB$LBSTRESU[3]=NA
+
+ expect_false(check_lb_lbstresu(LB, DM))
+
+})
+
+
+
+test_that("Function returns false when expected column not present, DM is present with SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ DM <- data.frame(
+ USUBJID = 1:10,
+ SITEID = 111:120,
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESU=NULL
+
+ expect_false(check_lb_lbstresu(LB, DM))
+
+})
+
+
+
+test_that("Function returns true when no errors are present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ DM2 <- data.frame(
+ USUBJID = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ expect_true(check_lb_lbstresu(LB, DM2))
+})
+
+
+
+test_that("Function returns false when errors are present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESU[1]=""
+ LB$LBSTRESU[2]="NA"
+ LB$LBSTRESU[3]=NA
+
+ DM2 <- data.frame(
+ USUBJID = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ expect_false(check_lb_lbstresu(LB, DM2))
+
+})
+
+
+
+test_that("Function returns false when expected column not present, DM is present without SITEID variable", {
+
+ LB <- data.frame(
+ USUBJID = 1:10,
+ LBSTRESC = "5",
+ LBSTRESN = 1:10,
+ LBORRES = "5",
+ LBSTRESU = "g/L",
+ LBTESTCD = "ALB",
+ LBDTC = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ LB$LBSTRESU=NULL
+
+ DM2 <- data.frame(
+ USUBJID = 1:10,
+ stringsAsFactors=FALSE
+ )
+
+ expect_false(check_lb_lbstresu(LB, DM2))
+
+})
+
- LB <- data.frame(
- USUBJID = 1:10,
- LBSTRESC = "5",
- LBSTRESN = 1:10,
- LBORRES = "5",
- LBSTRESU = "g/L",
- LBTESTCD = "ALB",
- LBDTC = 1:10,
- stringsAsFactors=FALSE
- )
-
- LB$LBSTRESU=NULL
-
- expect_false(check_lb_lbstresu(LB))
-
- })
From 83f45bfb88a76d206e85ad6f14ba4bffdb244dc4 Mon Sep 17 00:00:00 2001
From: AlcJ123 <AlcJ123@users.noreply.github.com>
Date: Thu, 25 Jul 2024 01:36:54 +0000
Subject: [PATCH 4/4] Update documentation
---
man/check_lb_lbstresn_missing.Rd | 17 +++++++++--------
man/check_lb_lbstresu.Rd | 20 ++++++++++++--------
2 files changed, 21 insertions(+), 16 deletions(-)
diff --git a/man/check_lb_lbstresn_missing.Rd b/man/check_lb_lbstresn_missing.Rd
index fd0bb46f..2e4616d4 100644
--- a/man/check_lb_lbstresn_missing.Rd
+++ b/man/check_lb_lbstresn_missing.Rd
@@ -4,13 +4,13 @@
\alias{check_lb_lbstresn_missing}
\title{Check missing standard lab values (LBSTRESN/LBSTRESC)}
\usage{
-check_lb_lbstresn_missing(LB, DM, preproc = identity, ...)
+check_lb_lbstresn_missing(LB, DM = NULL, preproc = identity, ...)
}
\arguments{
\item{LB}{Lab SDTM dataset with variables USUBJID, LBTESTCD, LBDTC, LBORRES,
LBORRESU, LBSTRESN, LBSTRESC, VISIT (optional), LBSPID (optional)}
-\item{DM}{Demographics SDTM with variables USUBJID, SITEID}
+\item{DM}{Demographics SDTM with variables USUBJID, SITEID. Set to NULL.}
\item{preproc}{An optional company specific preprocessing script}
@@ -50,28 +50,29 @@ LB <- data.frame(
stringsAsFactors=FALSE
)
-check_lb_lbstresn_missing(LB, DM)
+check_lb_lbstresn_missing(LB)
LB$LBSTRESC[3] = ""
+check_lb_lbstresn_missing(LB)
+
check_lb_lbstresn_missing(LB, DM)
-LB$LBSTRESC[3] = ""
check_lb_lbstresn_missing(LB, DM2)
LB$LBSTRESC[1] = ""
-check_lb_lbstresn_missing(LB, DM)
+check_lb_lbstresn_missing(LB)
LB$VISIT = "SCREENING"
-check_lb_lbstresn_missing(LB, DM)
+check_lb_lbstresn_missing(LB)
LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
check_lb_lbstresn_missing(LB,preproc=roche_derive_rave_row)
LB$LBSTRESN = NULL
-check_lb_lbstresn_missing(LB, DM)
+check_lb_lbstresn_missing(LB)
LB$LBSTRESC = NULL
-check_lb_lbstresn_missing(LB, DM)
+check_lb_lbstresn_missing(LB)
}
\author{
diff --git a/man/check_lb_lbstresu.Rd b/man/check_lb_lbstresu.Rd
index ecee4a4e..6834d75f 100644
--- a/man/check_lb_lbstresu.Rd
+++ b/man/check_lb_lbstresu.Rd
@@ -4,14 +4,14 @@
\alias{check_lb_lbstresu}
\title{Check for missing lab units (LBSTRESU)}
\usage{
-check_lb_lbstresu(LB, DM, preproc = identity, ...)
+check_lb_lbstresu(LB, DM = NULL, preproc = identity, ...)
}
\arguments{
\item{LB}{Lab SDTM dataset with variables USUBJID, LBSTRESC, LBSTRESN,
LBORRES, LBSTRESU, LBTESTCD, LBDTC, LBMETHOD (optional),
LBSPID (optional), and VISIT (optional)}
-\item{DM}{Demographics SDTM with variables USUBJID, SITEID}
+\item{DM}{Demographics SDTM with variables USUBJID, SITEID. Set to NULL.}
\item{preproc}{An optional company specific preprocessing script}
@@ -52,28 +52,32 @@ stringsAsFactors=FALSE
)
-check_lb_lbstresu(LB, DM)
+check_lb_lbstresu(LB)
LB$LBSTRESU[1]=""
+check_lb_lbstresu(LB)
+
+check_lb_lbstresu(LB, DM2)
+
check_lb_lbstresu(LB, DM)
LB$LBSTRESU[1]=""
-check_lb_lbstresu(LB, DM2)
+check_lb_lbstresu(LB)
LB$LBSTRESU[2]="NA"
-check_lb_lbstresu(LB, DM)
+check_lb_lbstresu(LB)
LB$LBSTRESU[3]=NA
-check_lb_lbstresu(LB, DM)
+check_lb_lbstresu(LB)
LB$LBSPID= "FORMNAME-R:2/L:2XXXX"
check_lb_lbstresu(LB, DM, preproc=roche_derive_rave_row)
LB$VISIT= "SCREENING"
-check_lb_lbstresu(LB, DM)
+check_lb_lbstresu(LB)
LB$LBSTRESU=NULL
-check_lb_lbstresu(LB, DM)
+check_lb_lbstresu(LB)
}
\author{