Main PR

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",

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"
 
 

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))
 

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()

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()

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()

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()

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",