R/check_ae_aerel.R
check_ae_aerel.RdFlag if patient has a record with null value of AEREL but AEREL1 - AERELN contain 'Y'/'N'/'NA', so a likely mapping issue or if AEREL is missing and there is no any AERELn variable or if AEREL has unexpected value
check_ae_aerel(AE, preproc = identity, ...)Adverse Events SDTM dataset with variables USUBJID, AESEQ, AETERM, AESTDTC, AEREL, AERELn, AESPID (if present)
An optional company specific preprocessing script
Other arguments passed to methods
boolean value if check failed or passed with 'msg' attribute if the test failed
AE <- data.frame(
STUDYID = 1001,
USUBJID = c(1,2,3,1,2,3),
AESTDTC = rep('2020-05-05',6),
AETERM = c("abc Covid-19", "covid TEST POSITIVE","CHILLS"),
AESEQ = c(1,1,1,2,2,2),
AEREL = c("Y", "N", "NA", "N", "N", "Y"),
AEREL1 = c("Y", "N", "NA", "N", "NA", "Y"),
AEREL2 = c("Y", "N", "NA", "N", "N", "N"),
AESPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE
)
check_ae_aerel(AE)
#> [1] TRUE
AE1 <- data.frame(
STUDYID = 1001,
USUBJID = c(1,2,3,1,2,3),
AESTDTC = rep('2020-05-05',6),
AETERM = c("abc Covid-19", "covid TEST POSITIVE","CHILLS"),
AESEQ = c(1,1,1,2,2,2),
AEREL = c("Y", "N", "N", "N", "N", "N"),
AEREL1 = c("Y", "N", "NA", "N", "N", ""),
AEREL2 = c("Y", "N", " ", "N", "N", " "),
AESPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE
)
check_ae_aerel(AE1)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM AEREL AEREL1 AEREL2
#> 1 3 2020-05-05 CHILLS N NA
#> 2 3 2020-05-05 CHILLS N
check_ae_aerel(AE1,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM RAVE AEREL AEREL1 AEREL2
#> 1 3 2020-05-05 CHILLS FORMNAME-R:13 N NA
#> 2 3 2020-05-05 CHILLS FORMNAME-R:13 N
AE2 <- data.frame(
STUDYID = 1001,
USUBJID = c(1,2,3,1,2,3),
AESTDTC = rep('2020-05-05',6),
AETERM = c("abc Covid-19", "covid TEST POSITIVE","CHILLS"),
AESEQ = c(1,1,1,2,2,2),
AEREL = c("Y", "N", " ", "N", "N", " "),
AEREL1 = c("NA", "N", "NA", "Y", "N", " "),
AEREL2 = c("Y", "N", " ", "N", "N", " "),
AESPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE
)
check_ae_aerel(AE2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM AEREL AEREL1 AEREL2
#> 1 1 2020-05-05 abc Covid-19 N Y N
#> 2 3 2020-05-05 CHILLS NA
check_ae_aerel(AE2,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 2 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM RAVE AEREL AEREL1 AEREL2
#> 1 1 2020-05-05 abc Covid-19 FORMNAME-R:13 N Y N
#> 2 3 2020-05-05 CHILLS FORMNAME-R:13 NA
AE3 <- data.frame(
STUDYID = 1001,
USUBJID = c(1,2,3,1,2,3),
AESTDTC = rep('2020-05-05',6),
AETERM = c("abc Covid-19", "covid TEST POSITIVE","CHILLS"),
AESEQ = c(1,1,1,2,2,2),
AEREL = c("Y", " ", " ", "N", " ", "NA"),
AESPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE
)
check_ae_aerel(AE3)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM AEREL
#> 1 2 2020-05-05 covid TEST POSITIVE
#> 2 3 2020-05-05 CHILLS
#> 3 2 2020-05-05 covid TEST POSITIVE
check_ae_aerel(AE3,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 3 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM RAVE AEREL
#> 1 2 2020-05-05 covid TEST POSITIVE FORMNAME-R:13
#> 2 3 2020-05-05 CHILLS FORMNAME-R:13
#> 3 2 2020-05-05 covid TEST POSITIVE FORMNAME-R:13
AE4 <- data.frame(
STUDYID = 1001,
USUBJID = c(1,2,3,4,5,6),
AESTDTC = rep('2020-05-05',6),
AETERM = c("abc Covid-19", "covid TEST POSITIVE","CHILLS"),
AESEQ = c(1,2,3,4,5,6),
AEREL = c("Y", "Y", "N", "", "Y", "NA"),
AEREL1 = "",
AEREL2 = "",
AESPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE
)
check_ae_aerel(AE4)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 5 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM AEREL AEREL1 AEREL2
#> 1 1 2020-05-05 abc Covid-19 Y
#> 2 2 2020-05-05 covid TEST POSITIVE Y
#> 3 5 2020-05-05 covid TEST POSITIVE Y
#> 4 3 2020-05-05 CHILLS N
#> 5 4 2020-05-05 abc Covid-19
check_ae_aerel(AE4,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "AE has 5 observations where AEREL is missing but one of AEREL1 - AEREL[n] is equal to Y/N/NA, or AEREL has an unexpected value, or AEREL[n] missing. "
#> attr(,"data")
#> USUBJID AESTDTC AETERM RAVE AEREL AEREL1 AEREL2
#> 1 1 2020-05-05 abc Covid-19 FORMNAME-R:13 Y
#> 2 2 2020-05-05 covid TEST POSITIVE FORMNAME-R:13 Y
#> 3 5 2020-05-05 covid TEST POSITIVE FORMNAME-R:13 Y
#> 4 3 2020-05-05 CHILLS FORMNAME-R:13 N
#> 5 4 2020-05-05 abc Covid-19 FORMNAME-R:13