diff --git a/DESCRIPTION b/DESCRIPTION
index 9930d59..0a112fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: sdtmchecks
Title: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets
-Version: 1.0.0
+Version: 1.0.0.01
Authors@R: c(
person(given="Will",
family="Harris",
diff --git a/NEWS.md b/NEWS.md
index 3505510..7d317b5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# sdtmchecks 1.0.0.01 "CRAN Try"
+
+## Refinements of existing data check functions
+
+* Updates to several ophthalmology related checks
+
+
# sdtmchecks 1.0.0 "CRAN Try"
diff --git a/R/check_cm_cmlat.R b/R/check_cm_cmlat.R
index 0a496e4..fc56895 100644
--- a/R/check_cm_cmlat.R
+++ b/R/check_cm_cmlat.R
@@ -82,14 +82,32 @@ check_cm_cmlat <- function(CM,preproc = identity,...) {
mydf = CM %>%
filter(CMCAT == "CONCOMITANT MEDICATIONS") %>%
- mutate(MISFLAG = ifelse((toupper(CMROUTE) %in% c("OPHTHALMIC", "INTRAVITREAL", "INTRAOCULAR",
- "CONJUNCTIVAL", "INTRACAMERAL", "INTRACORNEAL",
- "RETROBULBAR", "SUBTENON", "SUBRETINAL",
- "SUBCONJUNCTIVAL") &
+ mutate(MISFLAG = ifelse((toupper(CMROUTE) %in% c("CONJUNCTIVAL",
+ "INTRACAMERAL",
+ "INTRACORNEAL",
+ "INTRAOCULAR",
+ "INTRAVITREAL",
+ "INTRAVITREAL VIA OCULAR IMPLANT",
+ "OPHTHALMIC",
+ "RETROBULBAR",
+ "SUBCONJUNCTIVAL",
+ "SUBRETINAL",
+ "SUBTENON",
+ "SUPRACHOROIDAL",
+ "TOPICAL") &
!(toupper(CMLAT) %in% c("LEFT", "RIGHT", "BILATERAL"))) |
- (!(toupper(CMROUTE) %in% c("OPHTHALMIC", "INTRAVITREAL", "INTRAOCULAR",
- "CONJUNCTIVAL", "INTRACAMERAL", "INTRACORNEAL",
- "RETROBULBAR", "SUBTENON", "SUBRETINAL",
+ (!(toupper(CMROUTE) %in% c("CONJUNCTIVAL",
+ "INTRACAMERAL",
+ "INTRACORNEAL",
+ "INTRAOCULAR",
+ "INTRAVITREAL",
+ "INTRAVITREAL VIA OCULAR IMPLANT",
+ "OPHTHALMIC",
+ "RETROBULBAR",
+ "SUBCONJUNCTIVAL",
+ "SUBRETINAL",
+ "SUBTENON",
+ "SUPRACHOROIDAL",
"TOPICAL")) &
(toupper(CMLAT) %in% c("LEFT", "RIGHT", "BILATERAL"))), 1, 0))
diff --git a/R/check_ec_sc_lat.R b/R/check_ec_sc_lat.R
index de31f76..5d19127 100644
--- a/R/check_ec_sc_lat.R
+++ b/R/check_ec_sc_lat.R
@@ -7,10 +7,10 @@
#' assuming drug administration is collected for study eye only.
#' 2.> Subset Subject Characteristics dataset (SC) for only Study Eye Selection
#' 3.> Compare Exposure dataset laterality (EC.ECLAT) with Subject Characteristics dataset laterality
-#' (SC.SCORRES - OS = LEFT, OD = RIGHT) and report if there is any mismatch.
+#' (SC.SCSTRESC - OS = LEFT, OD = RIGHT) and report if there is any mismatch.
#'
#' @param SC Subject Characteristics Dataset for Ophtha Study with variables
-#' USUBJID, SCTEST, SCTESTCD, SCCAT, SCORRES, SCDTC
+#' USUBJID, SCTEST, SCTESTCD, SCCAT, SCSTRESC, SCDTC
#' @param EC Subject Exposure Dataset with variables
#' USUBJID, ECCAT (if available), ECLOC, ECMOOD, ECLAT, ECSTDY, VISIT, ECSTDTC, ECOCCUR, ECROUTE
#'
@@ -34,7 +34,7 @@
#' SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
#' SCDTC = "2021-01-01",
#' stringsAsFactors = FALSE)
#'
@@ -67,7 +67,7 @@
#' SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
#' SCDTC = "2021-01-01",
#' stringsAsFactors = FALSE)
#'
@@ -102,7 +102,7 @@
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION",
#' "STUDY EYE SELECTION", "", "STUDY EYE SELECTION"),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
#' SCDTC = "2021-01-01",
#' stringsAsFactors = FALSE)
#'
@@ -127,9 +127,9 @@
check_ec_sc_lat <- function(EC,SC) {
- if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCORRES", "SCDTC")) {
+ if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCSTRESC", "SCDTC")) {
- fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCORRES", "SCDTC")))
+ fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCSTRESC", "SCDTC")))
}
@@ -164,13 +164,13 @@ check_ec_sc_lat <- function(EC,SC) {
}
# Subset SC data on SC.SCCAT = "STUDY EYE SELECTION", and
- # SCTESTCD = "FOCID". SC.SCORRES OS (oculus sinister) means the left
+ # SCTESTCD = "FOCID". SC.SCSTRESC OS (oculus sinister) means the left
# eye and OD (oculus dextrus) means the right eye.
SC <- SC %>%
- select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC) %>%
+ select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC) %>%
filter(toupper(SCTESTCD) == "FOCID") %>%
- mutate(SC_STUDYEYE = ifelse(toupper(SCORRES) == "OS", "LEFT",
- ifelse(toupper(SCORRES) == "OD", "RIGHT","SCORRES Value not OS or OD")))
+ mutate(SC_STUDYEYE = ifelse(toupper(SCSTRESC) == "OS", "LEFT",
+ ifelse(toupper(SCSTRESC) == "OD", "RIGHT","SCSTRESC Value not OS or OD")))
# Subset EC data on EC.ECCAT (if available) remove Fellow Eye Records,
# EC.ECMOOD = "PERFORMED" EC.ECOCCUR = "Y"
@@ -197,7 +197,7 @@ check_ec_sc_lat <- function(EC,SC) {
mydf = mydf1 %>% filter(MISFLAG == 1)%>%
filter(ECROUTE != "NON-OCULAR ROUTE" | is.na(ECROUTE)) %>%
- select(-MISFLAG, -SCTESTCD, -SCTEST, -SCCAT, -ECLOC, -ECMOOD, -ECOCCUR, -SCORRES)
+ select(-MISFLAG, -SCTESTCD, -SCTEST, -SCCAT, -ECLOC, -ECMOOD, -ECOCCUR, -SCSTRESC)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
diff --git a/R/check_oe_sc_lat_count_fingers.R b/R/check_oe_sc_lat_count_fingers.R
index cbc4d74..9a73287 100644
--- a/R/check_oe_sc_lat_count_fingers.R
+++ b/R/check_oe_sc_lat_count_fingers.R
@@ -3,7 +3,7 @@
#' @description Check If Post Treatment Count Fingers in Study Eye is done on the actual Study eye by comparing laterality from OE domain with SC domain.
#' Check is ignored if Post Treatment Count Fingers is not collected in study as it is quite common for EP studies
#'
-#' @param SC Subject Characteristics Dataset for Ophtho Study with variables USUBJID, SCTEST, SCTESTCD, SCCAT, SCORRES, SCDTC
+#' @param SC Subject Characteristics Dataset for Ophtho Study with variables USUBJID, SCTEST, SCTESTCD, SCCAT, SCSTRESC, SCDTC
#' @param OE Ophthalmic Examination Dataset for Ophtho Study with variables USUBJID, OECAT, OELAT, VISIT, OEDTC, OETEST, OELOC, OESTAT (if present)
#'
#' @importFrom dplyr %>% filter mutate select
@@ -30,7 +30,7 @@
#' SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
#' SCDTC = rep("2021-01-01", 6),
#' stringsAsFactors = FALSE)
#'
@@ -60,7 +60,7 @@
#' SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
#' SCDTC = rep("2021-01-01", 6),
#' stringsAsFactors = FALSE)
#'
@@ -93,7 +93,7 @@
#' SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
#' "STUDY EYE SELECTION", "STUDY EYE SELECTION",
#' "", "STUDY EYE SELECTION"),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
#' SCDTC = "2021-01-01",
#' stringsAsFactors = FALSE)
#'
@@ -119,9 +119,9 @@
check_oe_sc_lat_count_fingers <- function(OE, SC) {
- if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCORRES", "SCDTC")) {
+ if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCSTRESC", "SCDTC")) {
- fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCORRES", "SCDTC")))
+ fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCSTRESC", "SCDTC")))
}
@@ -138,12 +138,12 @@ check_oe_sc_lat_count_fingers <- function(OE, SC) {
else {
- # Subset SC data on SC.SCCAT = "STUDY EYE SELECTION", and and SCTESTCD = "FOCID". SC.SCORRES OS (oculus sinister) means the left
+ # Subset SC data on SC.SCCAT = "STUDY EYE SELECTION", and and SCTESTCD = "FOCID". SC.SCSTRESC OS (oculus sinister) means the left
# eye and OD (oculus dextrus) means the right eye.
- SC <- SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC) %>%
+ SC <- SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC) %>%
filter(SCTESTCD %in% c("FOCID")) %>%
- mutate(SC_STUDYEYE = ifelse(SCORRES == "OS", "LEFT",
- ifelse(SCORRES == "OD", "RIGHT", "SCORRES Value not OS or OD")))
+ mutate(SC_STUDYEYE = ifelse(SCSTRESC == "OS", "LEFT",
+ ifelse(SCSTRESC == "OD", "RIGHT", "SCSTRESC Value not OS or OD")))
# Remove OESTAT NOT DONE
if ((any(names(OE) == "OESTAT")) == TRUE) {
@@ -166,7 +166,7 @@ check_oe_sc_lat_count_fingers <- function(OE, SC) {
mydf1 <- left_join(SC, OE, by="USUBJID") %>%
mutate(MISFLAG = ifelse((toupper(SC_STUDYEYE) != toupper(OELAT)) | is.na(toupper(OELAT)), 1, 0))
- mydf = mydf1 %>% filter(MISFLAG == 1) %>% select(-MISFLAG, -SCTESTCD, -SCTEST, -SCCAT, -SCORRES, -OELOC, -OECAT)
+ mydf = mydf1 %>% filter(MISFLAG == 1) %>% select(-MISFLAG, -SCTESTCD, -SCTEST, -SCCAT, -SCSTRESC, -OELOC, -OECAT)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
diff --git a/R/check_sc_dm_eligcrit.R b/R/check_sc_dm_eligcrit.R
index 381c115..e465f86 100644
--- a/R/check_sc_dm_eligcrit.R
+++ b/R/check_sc_dm_eligcrit.R
@@ -1,13 +1,13 @@
#' @title Check SC Eye Meeting Eligibility Criteria assignments among DM patients
#'
#' @description Check if SC.SCCAT = "STUDY EYE SELECTION" and SC.SCTESTCD = "ELIGEYE",
-#' then SC.SCORRES should have "OS", "OD", or "OU" values. Flag if subject is in
-#' DM and without an associated SC.SCORRES value or the ELIGEYE Eye Meeting
+#' then SC.SCSTRESC should have "OS", "OD", or "OU" values. Flag if subject is in
+#' DM and without an associated SC.SCSTRESC value or the ELIGEYE Eye Meeting
#' Eligibility Criteria value is not "OS", "OD", or "OU".
#'
#' @param DM Subject Demographics SDTM dataset with variable USUBJID
#' @param SC Subject Characteristics SDTM dataset for Ophtho Study with variables
-#' USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC
+#' USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC
#'
#' @importFrom dplyr %>% filter mutate select left_join
#'
@@ -37,17 +37,17 @@
#' "STUDY EYE SELECTION",
#' "STUDY EYE SELECTION",
#' ""),
-#' SCORRES = c("OS", "OS", "", "", "OU", ""),
+#' SCSTRESC = c("OS", "OS", "", "", "OU", ""),
#' SCDTC = rep("2021-01-01", 6),
#' stringsAsFactors = FALSE)
#'
#' check_sc_dm_eligcrit(SC=sc, DM=dm)
#'
#' dm <- data.frame(USUBJID = c(1,2,3,4))
-#' sc$SCORRES[4] = "OS"
+#' sc$SCSTRESC[4] = "OS"
#' check_sc_dm_eligcrit(SC=sc, DM=dm)
#'
-#' sc$SCORRES <- NULL
+#' sc$SCSTRESC <- NULL
#' check_sc_dm_eligcrit(SC=sc, DM=dm)
#'
#'
@@ -61,22 +61,22 @@ check_sc_dm_eligcrit <- function(DM, SC) {
}
- else if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCORRES", "SCDTC")) {
+ else if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCSTRESC", "SCDTC")) {
- fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCORRES", "SCDTC")))
+ fail(lacks_msg(SC, c("USUBJID","SCTEST","SCTESTCD","SCCAT","SCSTRESC", "SCDTC")))
}
else {
DM = DM %>% select(USUBJID)
- SC = SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC) %>%
+ SC = SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC) %>%
mutate(MISFLAG = ifelse((grepl("ELIGEYE", SCTESTCD, ignore.case=TRUE) == TRUE) &
- (!(SCORRES %in% c("OD", "OS", "OU"))), 1, 0))
+ (!(SCSTRESC %in% c("OD", "OS", "OU"))), 1, 0))
mydf = left_join(DM, SC, by="USUBJID")
- mydf = mydf %>% filter(MISFLAG == 1 | is.na(SCORRES)) %>% select(-MISFLAG)
+ mydf = mydf %>% filter(MISFLAG == 1 | is.na(SCSTRESC)) %>% select(-MISFLAG)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
diff --git a/R/check_sc_dm_seyeselc.R b/R/check_sc_dm_seyeselc.R
index 0d8ca79..2e73686 100644
--- a/R/check_sc_dm_seyeselc.R
+++ b/R/check_sc_dm_seyeselc.R
@@ -1,13 +1,13 @@
#' @title Check SC Study Eye Selection assignments among DM patients
#'
#' @description Check if SC.SCCAT = "STUDY EYE SELECTION" and SC.SCTESTCD = "FOCID",
-#' then SC.SCORRES should have "OS", "OD", or "OU" values. Flag if subject is in
-#' DM and without an associated SC.SCORRES value or the STUDY EYE SELECTION value
-#' is not "OS", "OD", or "OU".
+#' then SC.SCSTRESC should have "OS" or "OD" values. Flag if subject is in
+#' DM and without an associated SC.SCSTRESC value or the STUDY EYE SELECTION value
+#' is not "OS" or "OD".
#'
#' @param DM Subject Demographics SDTM dataset with variable USUBJID
#' @param SC Subject Characteristics SDTM dataset for Ophtho Study with variables
-#' USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC
+#' USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC
#'
#' @importFrom dplyr %>% filter mutate select
#'
@@ -36,7 +36,7 @@
#' "",
#' "STUDY EYE SELECTION",
#' "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
#' SCDTC = rep("2021-01-01", 6),
#' stringsAsFactors = FALSE)
#'
@@ -56,7 +56,7 @@
#' "",
#' "STUDY EYE SELECTION",
#' "STUDY EYE SELECTION", ""),
-#' SCORRES = c("LEFT", "OS", "", "RIGHT", "", ""),
+#' SCSTRESC = c("LEFT", "OS", "", "RIGHT", "", ""),
#' SCDTC = rep("2021-01-01", 6),
#' stringsAsFactors = FALSE)
#'
@@ -73,22 +73,22 @@ check_sc_dm_seyeselc <- function(DM, SC) {
}
- else if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCORRES", "SCDTC")) {
+ else if (SC %lacks_any% c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCSTRESC", "SCDTC")) {
- fail(lacks_msg(SC, c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCORRES", "SCDTC")))
+ fail(lacks_msg(SC, c("USUBJID", "SCTEST", "SCTESTCD", "SCCAT", "SCSTRESC", "SCDTC")))
}
else {
DM = DM %>% select(USUBJID)
- SC = SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC) %>%
+ SC = SC %>% select(USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC) %>%
mutate(MISFLAG = ifelse((grepl("FOCID", SCTESTCD, ignore.case=TRUE) == TRUE) &
- (!(SCORRES %in% c("OD", "OS"))), 1, 0))
+ (!(SCSTRESC %in% c("OD", "OS"))), 1, 0))
mydf = left_join(DM, SC, by="USUBJID")
- mydf = mydf %>% filter(MISFLAG == 1 | is.na(SCORRES)) %>% select(-MISFLAG)
+ mydf = mydf %>% filter(MISFLAG == 1 | is.na(SCSTRESC)) %>% select(-MISFLAG)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
diff --git a/R/globals.R b/R/globals.R
index 350959b..876215c 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -14,7 +14,7 @@ utils::globalVariables(c(
"OESTRESN.y","OETESTCD","OETSTDTL","PARTB_CONST","PRCAT","PRENDTC","PRLAT","PROCCUR",
"PRPRESP","PRSTDTC","QSCAT","QSDTC","QSDTC1","QSORRES","QSREASND","QSSTAT","QSSTRESC",
"QSTESTCD","RAVE","REFTERM","ROW","ROWNUM","RSDTC","RSEVAL","RSORRES","RSSTAT","SCCAT","SCDTC",
-"SCORRES","SCTEST","SCTESTCD","SC_STUDYEYE","SITEID","SSDTC","SSORRES","SSSTAT","SYSBP",
+"SCORRES", "SCSTRESC", "SCTEST","SCTESTCD","SC_STUDYEYE","SITEID","SSDTC","SSORRES","SSSTAT","SYSBP",
"TOTAL","TOT_1M","TOT_4M","TRDTC","TREVAL","TRTESTCD","TSPARMCD","TSVAL","TUDTC","TUEVAL",
"TULOC","TUORRES","USUBJID","VISIT","VISITNUM","VSDTC","VSDTC.SYSBP","VSORRES","VSSPID",
"VSSTRESN","VSTEST","VSTESTCD","Var1","Var2","check_stat","icdate","issue",
diff --git a/man/check_ec_sc_lat.Rd b/man/check_ec_sc_lat.Rd
index 6a69c50..c9b43d9 100644
--- a/man/check_ec_sc_lat.Rd
+++ b/man/check_ec_sc_lat.Rd
@@ -11,7 +11,7 @@ check_ec_sc_lat(EC, SC)
USUBJID, ECCAT (if available), ECLOC, ECMOOD, ECLAT, ECSTDY, VISIT, ECSTDTC, ECOCCUR, ECROUTE}
\item{SC}{Subject Characteristics Dataset for Ophtha Study with variables
-USUBJID, SCTEST, SCTESTCD, SCCAT, SCORRES, SCDTC}
+USUBJID, SCTEST, SCTESTCD, SCCAT, SCSTRESC, SCDTC}
}
\value{
boolean value if check failed or passed with 'msg' attribute if the test failed
@@ -24,7 +24,7 @@ containing EC.ECCAT = “FELLOW”. If EC.ECCAT variable is not available then i
assuming drug administration is collected for study eye only.
2.> Subset Subject Characteristics dataset (SC) for only Study Eye Selection
3.> Compare Exposure dataset laterality (EC.ECLAT) with Subject Characteristics dataset laterality
-(SC.SCORRES - OS = LEFT, OD = RIGHT) and report if there is any mismatch.
+(SC.SCSTRESC - OS = LEFT, OD = RIGHT) and report if there is any mismatch.
}
\examples{
@@ -38,7 +38,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
@@ -71,7 +71,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
@@ -106,7 +106,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2,3),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", "", "STUDY EYE SELECTION"),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
diff --git a/man/check_oe_sc_lat_count_fingers.Rd b/man/check_oe_sc_lat_count_fingers.Rd
index f0adbff..4f37591 100644
--- a/man/check_oe_sc_lat_count_fingers.Rd
+++ b/man/check_oe_sc_lat_count_fingers.Rd
@@ -9,7 +9,7 @@ check_oe_sc_lat_count_fingers(OE, SC)
\arguments{
\item{OE}{Ophthalmic Examination Dataset for Ophtho Study with variables USUBJID, OECAT, OELAT, VISIT, OEDTC, OETEST, OELOC, OESTAT (if present)}
-\item{SC}{Subject Characteristics Dataset for Ophtho Study with variables USUBJID, SCTEST, SCTESTCD, SCCAT, SCORRES, SCDTC}
+\item{SC}{Subject Characteristics Dataset for Ophtho Study with variables USUBJID, SCTEST, SCTESTCD, SCCAT, SCSTRESC, SCDTC}
}
\value{
boolean value if check failed or passed with 'msg' attribute if the test failed
@@ -30,7 +30,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -60,7 +60,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -93,7 +93,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2,3),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION",
"", "STUDY EYE SELECTION"),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
diff --git a/man/check_sc_dm_eligcrit.Rd b/man/check_sc_dm_eligcrit.Rd
index 2aeb19d..d3236bb 100644
--- a/man/check_sc_dm_eligcrit.Rd
+++ b/man/check_sc_dm_eligcrit.Rd
@@ -10,15 +10,15 @@ check_sc_dm_eligcrit(DM, SC)
\item{DM}{Subject Demographics SDTM dataset with variable USUBJID}
\item{SC}{Subject Characteristics SDTM dataset for Ophtho Study with variables
-USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC}
+USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC}
}
\value{
boolean value if check failed or passed with 'msg' attribute if the test failed
}
\description{
Check if SC.SCCAT = "STUDY EYE SELECTION" and SC.SCTESTCD = "ELIGEYE",
-then SC.SCORRES should have "OS", "OD", or "OU" values. Flag if subject is in
-DM and without an associated SC.SCORRES value or the ELIGEYE Eye Meeting
+then SC.SCSTRESC should have "OS", "OD", or "OU" values. Flag if subject is in
+DM and without an associated SC.SCSTRESC value or the ELIGEYE Eye Meeting
Eligibility Criteria value is not "OS", "OD", or "OU".
}
\examples{
@@ -37,17 +37,17 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
"STUDY EYE SELECTION",
"STUDY EYE SELECTION",
""),
- SCORRES = c("OS", "OS", "", "", "OU", ""),
+ SCSTRESC = c("OS", "OS", "", "", "OU", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
check_sc_dm_eligcrit(SC=sc, DM=dm)
dm <- data.frame(USUBJID = c(1,2,3,4))
-sc$SCORRES[4] = "OS"
+sc$SCSTRESC[4] = "OS"
check_sc_dm_eligcrit(SC=sc, DM=dm)
-sc$SCORRES <- NULL
+sc$SCSTRESC <- NULL
check_sc_dm_eligcrit(SC=sc, DM=dm)
diff --git a/man/check_sc_dm_seyeselc.Rd b/man/check_sc_dm_seyeselc.Rd
index 98137db..6a92fc4 100644
--- a/man/check_sc_dm_seyeselc.Rd
+++ b/man/check_sc_dm_seyeselc.Rd
@@ -10,16 +10,16 @@ check_sc_dm_seyeselc(DM, SC)
\item{DM}{Subject Demographics SDTM dataset with variable USUBJID}
\item{SC}{Subject Characteristics SDTM dataset for Ophtho Study with variables
-USUBJID, SCTESTCD, SCTEST, SCCAT, SCORRES, SCDTC}
+USUBJID, SCTESTCD, SCTEST, SCCAT, SCSTRESC, SCDTC}
}
\value{
boolean value if check failed or passed with 'msg' attribute if the test failed
}
\description{
Check if SC.SCCAT = "STUDY EYE SELECTION" and SC.SCTESTCD = "FOCID",
-then SC.SCORRES should have "OS", "OD", or "OU" values. Flag if subject is in
-DM and without an associated SC.SCORRES value or the STUDY EYE SELECTION value
-is not "OS", "OD", or "OU".
+then SC.SCSTRESC should have "OS" or "OD" values. Flag if subject is in
+DM and without an associated SC.SCSTRESC value or the STUDY EYE SELECTION value
+is not "OS" or "OD".
}
\examples{
@@ -36,7 +36,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
"",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -56,7 +56,7 @@ sc <- data.frame(USUBJID = c(1,1,1,2,2,2),
"",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
diff --git a/tests/testthat/test-check_ec_sc_lat.R b/tests/testthat/test-check_ec_sc_lat.R
index e3ea411..eec6dec 100644
--- a/tests/testthat/test-check_ec_sc_lat.R
+++ b/tests/testthat/test-check_ec_sc_lat.R
@@ -11,7 +11,7 @@ test_that("Function returns true when no errors are present", {
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
@@ -47,7 +47,7 @@ test_that("Function returns false when errors are present", {
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
@@ -72,7 +72,7 @@ test_that("Function returns false when errors are present", {
})
-test_that("Function returns false when errors are present", {
+test_that("Function returns false when missing required variables", {
sc <- data.frame(USUBJID = c(1,1,1,2,2,2,3),
SCTEST = c("Eye Meeting Eligibility Criteria",
@@ -86,7 +86,7 @@ test_that("Function returns false when errors are present", {
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", "", "STUDY EYE SELECTION"),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "RIGHT"),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
diff --git a/tests/testthat/test-check_oe_sc_lat_count_fingers.R b/tests/testthat/test-check_oe_sc_lat_count_fingers.R
index 9cf505f..9615aac 100644
--- a/tests/testthat/test-check_oe_sc_lat_count_fingers.R
+++ b/tests/testthat/test-check_oe_sc_lat_count_fingers.R
@@ -10,7 +10,7 @@ test_that("Returns true when no errors present", {
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -44,7 +44,7 @@ test_that("Returns false when errors present - 1", {
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -81,7 +81,7 @@ test_that("Returns false when errors present - 2", {
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION",
"", "STUDY EYE SELECTION"),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", "", "OS"),
SCDTC = "2021-01-01",
stringsAsFactors = FALSE)
@@ -153,7 +153,7 @@ test_that("Returns false when expected column not present - 2", {
SCTESTCD = c("ELIGEYE", "FOCID", "", "ELIGEYE", "FOCID", ""),
SCCAT = c("STUDY EYE SELECTION", "STUDY EYE SELECTION", "",
"STUDY EYE SELECTION", "STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
diff --git a/tests/testthat/test-check_sc_dm_eligcrit.R b/tests/testthat/test-check_sc_dm_eligcrit.R
index 5360af1..612c3c1 100644
--- a/tests/testthat/test-check_sc_dm_eligcrit.R
+++ b/tests/testthat/test-check_sc_dm_eligcrit.R
@@ -14,11 +14,11 @@ test_that("Function returns true when no errors are present", {
"STUDY EYE SELECTION",
"STUDY EYE SELECTION",
""),
- SCORRES = c("OS", "OS", "", "", "OU", ""),
+ SCSTRESC = c("OS", "OS", "", "", "OU", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
- sc$SCORRES[4] = "OS"
+ sc$SCSTRESC[4] = "OS"
expect_true(check_sc_dm_eligcrit(SC=sc, DM=dm))
})
@@ -39,13 +39,13 @@ test_that("Function returns false when errors present", {
"STUDY EYE SELECTION",
"STUDY EYE SELECTION",
""),
- SCORRES = c("OS", "OS", "", "", "OU", ""),
+ SCSTRESC = c("OS", "OS", "", "", "OU", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
#missing values
dm <- data.frame(USUBJID = c(1,2,3,4))
- sc$SCORRES[4] = "OS"
+ sc$SCSTRESC[4] = "OS"
expect_false(check_sc_dm_eligcrit(SC=sc, DM=dm))
@@ -69,14 +69,13 @@ test_that("Function returns false when expected column not present",{
"STUDY EYE SELECTION",
"STUDY EYE SELECTION",
""),
- SCORRES = c("OS", "OS", "", "", "OU", ""),
+ SCSTRESC = c("OS", "OS", "", "", "OU", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
- sc$SCORRES <- NULL
+ sc$SCSTRESC <- NULL
expect_false(check_sc_dm_eligcrit(SC=sc, DM=dm))
})
-
\ No newline at end of file
diff --git a/tests/testthat/test-check_sc_dm_seyeselc.R b/tests/testthat/test-check_sc_dm_seyeselc.R
index 00c8e4e..6c6f4b8 100644
--- a/tests/testthat/test-check_sc_dm_seyeselc.R
+++ b/tests/testthat/test-check_sc_dm_seyeselc.R
@@ -12,7 +12,7 @@ test_that("Function returns true when no errors are present" ,{
"",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "OD", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "OD", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -34,7 +34,7 @@ test_that("Function returns false when errors present", {
"",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
@@ -57,11 +57,10 @@ test_that("Function returns false when expected column not present", {
"",
"STUDY EYE SELECTION",
"STUDY EYE SELECTION", ""),
- SCORRES = c("LEFT", "OS", "", "RIGHT", "", ""),
+ SCSTRESC = c("LEFT", "OS", "", "RIGHT", "", ""),
SCDTC = rep("2021-01-01", 6),
stringsAsFactors = FALSE)
- sc$SCORRES <- NULL
+ sc$SCSTRESC <- NULL
expect_false(check_sc_dm_eligcrit(SC=sc, DM=dm))
})
-
\ No newline at end of file