R/check_cm_cmindc.R

In sdtmchecks: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

#' @title Check for concomitant medication indication with text string "PROPHYL"
#' when not given for prophylaxis
#'
#' @description This check looks for patients with text string "PROPHYL" in CMINDC
#' when CMPROPH is not checked as "Y" in studies with given for prophylaxis
#' variable (CMPROPH)
#'
#' @param CM Concomitant Medication SDTM dataset with variables USUBJID, CMTRT,
#' CMSTDTC, CMINDC, CMPROPH, CMSPID (optional)
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
#' @importFrom dplyr %>% filter select
#' @importFrom tidyselect any_of
#'
#' @return boolean value if check failed or passed with 'msg' attribute if the
#'   test failed
#'
#' @export
#'
#'
#' @author Sara Bodach, Stella Banjo (HackR 2021)
#'
#' @examples
#'
#' CM <- data.frame(
#'  USUBJID = c(rep(1,3),rep(2,3),rep(3,3)),
#'  CMTRT = letters[1:9],
#'  CMSTDTC = rep("2017-01-01",9),
#'  CMINDC = c(rep("INDICATION 1",2), rep("indication 2",2),
#'             rep("Prophylaxis",2),rep("PROPHYLACTIC",2),"PROPHYLAXIS FOR XYZ"),
#'  CMPROPH = c(rep("Y",3),rep(NA,2),rep("",2),"NA","."),
#'  CMSPID = "/F:XXX-D:12345-R:123",
#'  stringsAsFactors=FALSE
#' )
#'
#' check_cm_cmindc(CM)
#' check_cm_cmindc(CM,preproc=roche_derive_rave_row)
#'
#' CM$CMPROPH[7] = "Y"
#' check_cm_cmindc(CM)
#'
#' CM$CMSPID = NULL
#' check_cm_cmindc(CM,preproc=roche_derive_rave_row)
#'
#' CM$CMPROPH = NULL
#' check_cm_cmindc(CM)
#'
#'

check_cm_cmindc <- function(CM,preproc=identity,...){

    ###First check that required variables exist and return a message if they don't
    if(CM %lacks_any% c("USUBJID", "CMTRT", "CMSTDTC","CMINDC", "CMPROPH")){

        fail(lacks_msg(CM, c("USUBJID", "CMTRT", "CMSTDTC","CMINDC", "CMPROPH")))

    } else{

        #Apply company specific preprocessing function
        CM = preproc(CM,...)

        perm_var <- c("RAVE")
        int_var <- intersect(names(CM), perm_var)

        # keep records not indicated as prophylactic via CMPROPH

        cmNP = CM %>%
            filter(is_sas_na(CMPROPH)) %>%
            select(any_of(c("USUBJID", int_var, "CMTRT", "CMSTDTC","CMINDC", "CMPROPH","RAVE")))

         mydf <- cmNP %>% filter(grepl("PROPHYL", toupper(CMINDC)))
         rownames(mydf)=NULL

         #check

         if (nrow(mydf)==0) {
             pass()
         } else {

             fail(paste0("There are ",length(unique(mydf$USUBJID)),
                        " patients with CM indication containing 'PROPHYL' when given for prophylaxis variable is not checked as 'Y'. "),
                  mydf)
         }
    }
}