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, ...)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