check_lb_lbdtc_visit_ordinal_error {sdtmchecks}

Check that all LB dates are duplicated or earlier than last visit's (possible datetime data entry error)

Description

This check identifies LBDTC values that are duplicated or earlier than last visit's. Records with LBSTAT == 'NOT DONE' and unscheduled visits (VISIT with the string "UNSCHEDU") and treatment discon visits (VISIT with the string "TREATMENT OR OBSERVATION FU COMP EARLY DISC") are excluded.

Usage

check_lb_lbdtc_visit_ordinal_error(LB)

Arguments

LB

SDTM dataset with variables USUBJID, VISITNUM, VISIT, LBDTC, LBTESTCD, LBSTAT

Value

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

Author(s)

Simon Luo

Examples

# no case
LB1 <- data.frame(USUBJID = c(rep("101", 5), rep("102", 5)),
                LBCAT = "Hematology",
                LBDTC = rep(c(
                "2017-01-01T08:25",
                "2017-01-05T09:25",
                "2017-01-15T10:25",
                "2017-01-20T08:25",
                "2017-01-25T08:25"), 2),
                VISITNUM = rep(1:5,2),
                VISIT = rep(c(
                "Visit 1",
                "Visit 2",
                "Visit 3",
                "UNSCheduled!!!",
                "VIsit 5"), 2),
                LBSTAT = c(rep("", 9), "NOT DONE"),
                stringsAsFactors = FALSE)

check_lb_lbdtc_visit_ordinal_error(LB1)

LB2 = LB1
LB2$LBCAT = "Virology"
LB3 <- rbind(LB1, LB2)
check_lb_lbdtc_visit_ordinal_error(LB3)

# adding cases with earlier date
LB3$LBDTC[LB3$USUBJID == 101 & LB3$VISIT == "Visit 3"] <- "2016-01-10T08:25"
LB3$LBDTC[LB3$USUBJID == 102 & LB3$VISIT == "Visit 2"] <- "2016-01-01T06:25"
check_lb_lbdtc_visit_ordinal_error(LB = LB3)

# adding cases with duplicated date
LB3$LBDTC[LB3$USUBJID == 102 & LB3$VISIT == "Visit 3"] <- "2017-01-15T10:25"
LB3 <- LB3[order(LB3$USUBJID, LB3$VISITNUM, LB3$LBDTC),]
check_lb_lbdtc_visit_ordinal_error(LB = LB3)

# check if all NOT DONE
LB4 = LB3
LB4$LBSTAT = "NOT DONE"
check_lb_lbdtc_visit_ordinal_error(LB = LB4)

# check dropping a required variable
LB4$LBSTAT = NULL
check_lb_lbdtc_visit_ordinal_error(LB = LB4)