Check for non-missing SSORRES if SSSTAT is NOT DONE

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)

check_ss_ssstat_ssorres(SS, preproc = identity, ...)

Arguments

SS

Long-Term Survival Follow-Up SDTM dataset with variables USUBJID, VISIT, SSSTAT, SSDTC, SSORRES, SSSPID (optional)

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Value

boolean value if check failed or passed with 'msg' attribute if the test failed

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)
#> [1] FALSE
#> attr(,"msg")
#> [1] "SS (LTFU) has 4 record(s) for 2 unique patient(s) with non-missing SSORRES when SSSTAT=NOT DONE (no contact).  "
#> attr(,"data")
#>   USUBJID                       VISIT      SSDTC SSORRES   SSSTAT
#> 1       1 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01    DEAD NOT DONE
#> 2       1 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE
#> 3       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01    DEAD NOT DONE
#> 4       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE

SS$SSORRES[2]=NA
check_ss_ssstat_ssorres(SS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "SS (LTFU) has 3 record(s) for 2 unique patient(s) with non-missing SSORRES when SSSTAT=NOT DONE (no contact).  "
#> attr(,"data")
#>   USUBJID                       VISIT      SSDTC SSORRES   SSSTAT
#> 1       1 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE
#> 2       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01    DEAD NOT DONE
#> 3       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE

SS$SSSPID="FORMNAME-R:5/L:5XXXX"
check_ss_ssstat_ssorres(SS,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "SS (LTFU) has 3 record(s) for 2 unique patient(s) with non-missing SSORRES when SSSTAT=NOT DONE (no contact).  "
#> attr(,"data")
#>   USUBJID                       VISIT      SSDTC SSORRES   SSSTAT         RAVE
#> 1       1 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE FORMNAME-R:5
#> 2       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01    DEAD NOT DONE FORMNAME-R:5
#> 3       2 SURVIVAL FOLLOW UP 3 MONTHS 2016-01-01       U NOT DONE FORMNAME-R:5

SS$SSORRES[6]=NA
SS$SSORRES[8]=""
SS$SSORRES[12]=NA
check_ss_ssstat_ssorres(SS)
#> [1] TRUE

SS$SSORRES=NULL
check_ss_ssstat_ssorres(SS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "SS is missing the variable: SSORRES"