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check_cm_cmlat.R
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check_cm_cmlat.R
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#' @title Check if ocular concomitant medication has laterality missing or laterality field is
#' populated but route is not eye-related.
#'
#' @description This check assesses CMCAT = "CONCOMITANT MEDICATIONS" and flags potential
#' ocular records with missing/inconsistent route and laterality: for eye-related
#' CMROUTE ('INTRAVITREAL', 'OPHTHALMIC', etc.), CMLAT is not populated -or- CMROUTE is not eye-related
#' (i.e., not INTRAVITREAL, OPHTHALMIC, TOPICAL, etc.) but CMLAT is LEFT/RIGHT/BILATERAL.
#'
#' @param CM Concomitant Medications Dataset for Ophtho Study with variables
#' USUBJID, CMCAT, CMLAT, CMDECOD, CMTRT, CMROUTE, CMSPID (if Present), CMSTDTC (if Present)
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
#' @importFrom dplyr %>% filter mutate select
#'
#' @family OPHTH
#'
#' @keywords OPHTH
#'
#' @export
#'
#' @author Monarch Shah (HackR 2021 Team Eye)
#'
#'
#' @examples
#'
#' CM <- data.frame(
#' USUBJID = 1:7,
#' CMCAT = "CONCOMITANT MEDICATIONS",
#' CMSTDTC = 1:7,
#' CMLAT = c("Left", "","Bilateral", "", "", "LEFT", ""),
#' CMTRT = c("A", "B", "A", "B", "A", "A", "B"),
#' CMDECOD = c("A", "B", "A", "B", "A", "A", "B"),
#' CMROUTE = c("","OPHTHALMIC","INTRAVITREAL","INTRAVITREAL",
#' "opHTHALMIC", "INTRaOCULAr", "INTRaOCULAr"),
#' CMSPID = "FORMNAME-R:13/L:13XXXX",
#' stringsAsFactors = FALSE)
#' check_cm_cmlat(CM,preproc=roche_derive_rave_row)
#'
#' CM <- data.frame(
#' USUBJID = 1:5,
#' CMCAT = rep("CONCOMITANT MEDICATIONS",5),
#' CMSTDTC = 1:5,
#' CMLAT = c("Left", "LEFT","Bilateral",
#' "RIGHT", "RIgHT"),
#' CMTRT = c("A", "B", "A", "B", "A"),
#' CMDECOD = c("A", "B", "A", "B", "A"),
#' CMROUTE = c("","OPHTHALMIC","INTRAVITREAL",
#' "INTRaOCULAr", "opHTHALMIC"),
#' stringsAsFactors = FALSE)
#' check_cm_cmlat(CM)
#'
#' CM <- data.frame(
#' USUBJID = 1:5,
#' CMCAT = "CONCOMITANT MEDICATIONS",
#' CMSTDTC = 1:5,
#' CMLAT = c("Left", "LEFT","Bilateral", "RIGHT", "RIgHT"),
#' CMTRT = c("A", "B", "A", "B", "A"),
#' CMDECOD = c("A", "B", "A", "B", "A"),
#' #CMROUTE = c("","OPHTHALMIC","INTRAVITREAL","INTRaOCULAr", "opHTHALMIC"),
#' stringsAsFactors = FALSE)
#' check_cm_cmlat(CM)
#'
check_cm_cmlat <- function(CM,preproc = identity,...) {
if (CM %lacks_any% c("USUBJID", "CMCAT", "CMLAT", "CMTRT", "CMDECOD", "CMROUTE")) {
fail(lacks_msg(CM, c("USUBJID", "CMCAT", "CMLAT", "CMTRT", "CMDECOD", "CMROUTE")))
}
else {
#Apply company specific preprocessing function
CM = preproc(CM,...)
perm_var <- c("CMSTDTC", "RAVE")
int_var <- intersect(names(CM), perm_var)
mydf = CM %>%
filter(CMCAT == "CONCOMITANT MEDICATIONS") %>%
mutate(MISFLAG = ifelse((toupper(CMROUTE) %in% c("OPHTHALMIC", "INTRAVITREAL", "INTRAOCULAR",
"CONJUNCTIVAL", "INTRACAMERAL", "INTRACORNEAL",
"RETROBULBAR", "SUBTENON", "SUBRETINAL",
"SUBCONJUNCTIVAL") &
!(toupper(CMLAT) %in% c("LEFT", "RIGHT", "BILATERAL"))) |
(!(toupper(CMROUTE) %in% c("OPHTHALMIC", "INTRAVITREAL", "INTRAOCULAR",
"CONJUNCTIVAL", "INTRACAMERAL", "INTRACORNEAL",
"RETROBULBAR", "SUBTENON", "SUBRETINAL",
"TOPICAL")) &
(toupper(CMLAT) %in% c("LEFT", "RIGHT", "BILATERAL"))), 1, 0))
my_select_var <- c("USUBJID", int_var, "CMLAT", "CMTRT", "CMDECOD", "CMROUTE", "MISFLAG")
mydf <- mydf[,my_select_var]
rownames(mydf)=NULL
mydf <- mydf %>% filter(MISFLAG == 1) %>% select(-MISFLAG)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
} else {
fail(paste(nrow(mydf),
"record(s) with CMLAT Missing when CM is Eye related, or CMLAT is LEFT/RIGHT/BILATERAL and CMROUTE is not Eye related."
), mydf )
}
}
}