sdtmchecks (version 1.0.0)

check_ae_aerel: Check for AEREL1 - AERELN when AEREL is missing and when AEREL is unexpected

Description

Flag 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

Usage

check_ae_aerel(AE, preproc = identity, ...)

Value

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

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AESEQ, AETERM, AESTDTC, AEREL, AERELn, AESPID (if present)

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Author

Vira Vrakina

Examples

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)

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)
check_ae_aerel(AE1,preproc=roche_derive_rave_row)

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)
check_ae_aerel(AE2,preproc=roche_derive_rave_row)

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)
check_ae_aerel(AE3,preproc=roche_derive_rave_row)


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)
check_ae_aerel(AE4,preproc=roche_derive_rave_row)