Check TR Longest Diameter Records where the same date occurs across multiple visits

Source: R/check_tr_trdtc_across_visit.R

This check identifies records where the same date TRDTC occurs across multiple visits for Longest Diameter measurements (TRTESTCD is "LDIAM"). Only applies to assessments by investigator, selected based on uppercased TREVAL = "INVESTIGATOR" or missing or TREVAL variable does not exist.

check_tr_trdtc_across_visit(TR, preproc = identity, ...)

Arguments

TR

Tumor Result SDTM dataset with variables USUBJID, TRDTC, TRTESTCD, VISIT, TREVAL (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

Will Harris

Examples


TR <- data.frame(
USUBJID = 1,
TRDTC = c(rep("2016-01-01",3), rep("2016-06-01",5), rep("2016-06-24",2)),
VISIT = c(rep("C1D1",3), rep("C1D2",3), rep("C2D1",4)),
TRTESTCD = c(rep("LDIAM",7),rep("SAXIS",3)),
TRSPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors=FALSE)

check_tr_trdtc_across_visit(TR)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 2 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD
#> 1       1 2016-06-01  C1D2    LDIAM
#> 2       1 2016-06-01  C2D1    LDIAM
check_tr_trdtc_across_visit(TR, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 2 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD          RAVE
#> 1       1 2016-06-01  C1D2    LDIAM FORMNAME-R:13
#> 2       1 2016-06-01  C2D1    LDIAM FORMNAME-R:13

TR2 <- TR
TR2$TRSPID[4:5] <- c("FORMNAME2-R:5/L:13XXXX", "FORMNAME3-R:0/L:13XXXX")

check_tr_trdtc_across_visit(TR2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 2 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD
#> 1       1 2016-06-01  C1D2    LDIAM
#> 2       1 2016-06-01  C2D1    LDIAM
check_tr_trdtc_across_visit(TR2, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 4 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD          RAVE
#> 1       1 2016-06-01  C1D2    LDIAM FORMNAME2-R:5
#> 2       1 2016-06-01  C1D2    LDIAM FORMNAME3-R:0
#> 3       1 2016-06-01  C1D2    LDIAM FORMNAME-R:13
#> 4       1 2016-06-01  C2D1    LDIAM FORMNAME-R:13

# missing optional variable
TR3 <- TR
TR3$TRSPID <- NULL

check_tr_trdtc_across_visit(TR3)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 2 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD
#> 1       1 2016-06-01  C1D2    LDIAM
#> 2       1 2016-06-01  C2D1    LDIAM
check_tr_trdtc_across_visit(TR3, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 2 TR Longest Diameter records where the same date occurs accross multiple visits. "
#> attr(,"data")
#>   USUBJID      TRDTC VISIT TRTESTCD
#> 1       1 2016-06-01  C1D2    LDIAM
#> 2       1 2016-06-01  C2D1    LDIAM

# missing required variable
TR4 <- TR
TR4$TRTESTCD <- NULL

check_tr_trdtc_across_visit(TR4)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TR is missing the variable: TRTESTCD"
check_tr_trdtc_across_visit(TR4, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TR is missing the variable: TRTESTCD"