R/check_tu_tudtc.R

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

#' @title Check for missing TUDTC values
#'
#' @description This check looks for missing TUDTC values and returns a data frame.
#'   Only applies to assessments by investigator.
#'
#' @param TU Tumor Identification SDTM dataset with variables USUBJID, TUDTC,
#' VISIT, TUORRES, TUSPID (optional), TUTESTCD (optional)
#' @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
#'
#' @author Beeya Na
#'
#' @examples
#' TU <- data.frame(
#' USUBJID = "1001",
#' TUDTC = "2020-05-05",
#' VISIT = "C1D1",
#' TUORRES = 1:10,
#' TUSPID = "FORMNAME-R:19/L:19XXXX",
#' TUEVAL = "INVESTIGATOR",
#' TUTESTCD = "TUMIDENT",
#' stringsAsFactors = FALSE
#' )
#'
#' TU$TUDTC[1]=""
#' TU$TUDTC[2]="NA"
#' TU$TUDTC[3]=NA
#'
#' check_tu_tudtc(TU,preproc=roche_derive_rave_row)
#'
#' TU$TUEVAL[1]=""
#' TU$TUTESTCD=NULL
#' check_tu_tudtc(TU,preproc=roche_derive_rave_row)
#'
#' TU$TUEVAL[2]="INDEPENDENT ASSESSOR"
#' TU$TUEVAL[3]="INDEPENDENT ASSESSOR"
#' TU$TUDTC[4]=""
#' check_tu_tudtc(TU)
#'
#' TU$TUSPID=NULL
#' check_tu_tudtc(TU)
#'
#' TU$VISIT=NULL
#' check_tu_tudtc(TU)
#'
#'

check_tu_tudtc <- function(TU,preproc=identity,...) {

    ###First check that required variables exist and return a message if they don't
    if(TU %lacks_any% c("USUBJID","TUDTC","VISIT","TUORRES")){

        fail(lacks_msg(TU, c("USUBJID","TUDTC","VISIT","TUORRES")))

    } else{

        #Apply company specific preprocessing function
        TU = preproc(TU,...)
        myvars <- c("USUBJID","VISIT","TUDTC","TUORRES", names(TU)[names(TU) %in% c("RAVE", "TUEVAL", "TUTESTCD")])

        TU <- subset(TU, select = myvars)

        if(TU %lacks_any% "TUEVAL"){

        ### Subset TU to only records with missing TUDTC
        mydf <- TU %>%
                filter(is_sas_na(TUDTC))
        }else{
        mydf <- TU %>%
            filter(is_sas_na(TUDTC),toupper(TUEVAL) == "INVESTIGATOR" | is_sas_na(TUEVAL))
        }

        rownames(mydf)=NULL

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

            ### Return subset dataframe if there are records with missing TUDTC
            fail(paste("TU has", length(unique(mydf$USUBJID)),"patient(s) with", nrow(mydf),
                       "record(s) with missing TUDTC. "), mydf)
        }
    }
}