R/check_cm_cmdecod.R

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

#' @title Check for missing CMDECOD values
#'
#' @description This check looks for missing CMDECOD values
#'
#' @param CM Concomitant Medications SDTM dataset with variables USUBJID, CMTRT, CMDECOD
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
#' @return boolean value if check failed or passed with 'msg' attribute if the test failed
#'
#' @export
#'
#' @importFrom dplyr %>% filter select
#' @importFrom tidyselect any_of
#'
#' @author Lei Zhao, Stella Banjo (HackR 2021)
#'
#' @examples
#'
#' CM <- data.frame(
#'  USUBJID = 1:5,
#'  DOMAIN = rep("CM", 5),
#'  CMTRT = rep("DRUG TERM", 5),
#'  CMDECOD = rep("CODED DRUG TERM", 5),
#'  CMSTDTC = 1:5,
#'  CMENDTC = 1:5,
#'  CMCAT = "CONCOMITANT MEDICATIONS",
#'  CMSPID = c("FORMNAME-R:13/L:13XXXX",
#'              "FORMNAME-R:16/L:16XXXX",
#'              "FORMNAME-R:2/L:2XXXX",
#'              "FORMNAME-R:19/L:19XXXX",
#'              "FORMNAME-R:5/L:5XXXX"),
#'  stringsAsFactors=FALSE
#' )
#'
#' check_cm_cmdecod(CM)
#'
#' CM$CMDECOD[1] = NA
#' CM$CMDECOD[2] = "NA"
#' CM$CMDECOD[3:5] = ""
#' check_cm_cmdecod(CM)
#' check_cm_cmdecod(CM,preproc=roche_derive_rave_row)
#'
#' CM$CMDECOD <- NULL
#' check_cm_cmdecod(CM)
#'

check_cm_cmdecod <- 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","CMDECOD","CMCAT")){

    fail(lacks_msg(CM, c("USUBJID","CMTRT","CMDECOD","CMCAT")))

  }else {

    #Apply company specific pre-processing function
    CM = preproc(CM,...)

    ### Subset domain to only records with missing coded term (CMDECOD)
    mydf <- CM %>%
      filter(grepl("CONCOMITANT",CMCAT)) %>%
      select(any_of(c("USUBJID", "CMSTDTC", "CMTRT", "CMDECOD", "CMPRESP", "CMOCCUR", "RAVE"))) %>%
      filter(is_sas_na(CMDECOD))
    rownames(mydf)=NULL

    ###Print to report
    ### Return message if no records with missing CMDECOD
    if(nrow(mydf)==0){
      pass()
      ### Return subset dataframe if there are records with missing CMDECOD
    }else if(nrow(mydf)>0){
      fail(paste("CM has ",nrow(mydf)," record(s) with missing CMDECOD. ",
                 sep=""), mydf)
    }
  }
}