R/check_ss_ssstat_ssorres.R

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

#' @title Check for non-missing SSORRES if SSSTAT is NOT DONE
#'
#' @description This check is for studies with LTFU mapped to the SS domain,
#' check that if 'NOT DONE' (Unable to Contact), then there should not be
#' a response (SSORRES)
#'
#' @param SS Long-Term Survival Follow-Up SDTM dataset with variables USUBJID,
#' VISIT, SSSTAT, SSDTC, SSORRES, SSSPID (optional)
#' @param preproc An optional company specific preprocessing script
#' @param ... Other arguments passed to methods
#'
#' @importFrom dplyr %>% filter select arrange
#' @importFrom tidyselect any_of
#'
#' @return boolean value if check failed or passed with 'msg' attribute if the
#'   test failed
#'
#' @export
#'
#' @author Sara Bodach
#'
#' @examples
#'
#' SS <- data.frame(
#' STUDYID = 1,
#' USUBJID = c(rep(1,6),rep(2,6)),
#' SSSTRESC = c("ALIVE", "DEAD", "ALIVE", "", "", "U"),
#' SSORRES = c("ALIVE", "DEAD", "ALIVE", "", "", "U"),
#' VISIT = rep(c("SURVIVAL FOLLOW UP 3 MONTHS"),6),
#' SSSTAT = rep(c("","NOT DONE"),6),
#' SSDTC = "2016-01-01",
#' SSSPID = "",
#' stringsAsFactors = FALSE
#' )
#'
#' check_ss_ssstat_ssorres(SS)
#'
#' SS$SSORRES[2]=NA
#' check_ss_ssstat_ssorres(SS)
#'
#' SS$SSSPID="FORMNAME-R:5/L:5XXXX"
#' check_ss_ssstat_ssorres(SS,preproc=roche_derive_rave_row)
#'
#' SS$SSORRES[6]=NA
#' SS$SSORRES[8]=""
#' SS$SSORRES[12]=NA
#' check_ss_ssstat_ssorres(SS)
#'
#' SS$SSORRES=NULL
#' check_ss_ssstat_ssorres(SS)
#'
#'

check_ss_ssstat_ssorres <- function(SS,preproc=identity,...){

    ###First check that required variables exist and return a message if they don't
    if( SS %lacks_any% c("USUBJID", "SSORRES", "VISIT", "SSSTAT", "SSDTC") ){

        fail(lacks_msg(SS, c("USUBJID", "SSORRES", "VISIT", "SSSTAT", "SSDTC")))

    } else{

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

        mydf <- SS %>%
            ## Subset to required and optional variables
            select(any_of(c("USUBJID", "VISIT", "SSDTC", "SSORRES", "SSSTAT", "RAVE"))) %>%
            # potential future refinement - exclude 'U' and 'UNKNOWN' result
            # use SSORRES, variable used for LSTALVDT
                filter(SSSTAT=="NOT DONE" & !is_sas_na(SSORRES)) %>%
                arrange(USUBJID, SSDTC, VISIT) %>%
            unique()

        rownames(mydf)=NULL

        ###Print to report

        ### Return message if no records with issue in SS
        if(nrow(mydf)==0){
            pass()

            ### Return subset dataframe if there are issues in SS with NOT DONE but results
        } else if(nrow(mydf)>0){
            fail(paste0("SS (LTFU) has ", nrow(mydf), " record(s) for ", length(unique(mydf$USUBJID)),
                        " unique patient(s) with non-missing SSORRES when SSSTAT=NOT DONE (no contact). ",sep=" "),
                 mydf)
        }
    }
}