Check for TR records with missing TRSTRESN for Longest Diameter (LDIAM)

Source: R/check_tr_trstresn_ldiam.R

This checks looks for TR records with missing values in numeric result/finding for the Longest Diameter (TRTESTCD is LDIAM) tumor measurement. Only applies to assessments by investigator, selected based on uppercased TREVAL = "INVESTIGATOR" or missing or TREVAL variable does not exist.

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

Arguments

TR

Tumor Results SDTM dataset with variables USUBJID, TRTESTCD, TRLINKID/TRLNKID, TRDTC, VISIT, TRORRES, TRSTRESN, TREVAL (optional), TRSTAT (optional), TRSPID (optional)

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Value

Boolean value for whether the check passed or failed, with 'msg' attribute if the check failed

Author

Will Harris

Examples


TR <- data.frame(USUBJID = 1:5,
                 TRTESTCD = c("OTHER", rep("LDIAM", 4)),
                 TRLINKID = 1:5,
                 TRDTC = 1:5,
                 VISIT = LETTERS[1:5],
                 TRORRES = LETTERS[1:5],
                 TRSTRESN = 1:5,
                 TRSTAT = "",
                 TREVAL = "INVESTIGATOR",
                 TRSPID = "FORMNAME-R:19/L:19XXXX",
                 stringsAsFactors = FALSE)

check_tr_trstresn_ldiam(TR)
#> [1] TRUE

TR1 <- TR
TR1$TRSTAT <- NULL
TR1$TREVAL <- NULL
TR1$TRSPID <- NULL

check_tr_trstresn_ldiam(TR1)
#> [1] TRUE

TR2 <- TR
TR2$TRSTRESN <- c("", "NA", NA, 1, 1)

check_tr_trstresn_ldiam(TR2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TR has 2 record(s) with missing TRSTRESN values for LDIAM assessment. 0 record(s) indicate 'NOT DONE'. 0 record(s) indicate 'NOT EVALUABLE'. 2 record(s) indicate done and evaluable but otherwise missing."
#> attr(,"data")
#>   USUBJID TRTESTCD TRDTC VISIT TRORRES TRSTRESN TRLINKID TRSTAT
#> 2       2    LDIAM     2     B       B       NA        2       
#> 3       3    LDIAM     3     C       C     <NA>        3       
check_tr_trstresn_ldiam(TR2,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TR has 2 record(s) with missing TRSTRESN values for LDIAM assessment. 0 record(s) indicate 'NOT DONE'. 0 record(s) indicate 'NOT EVALUABLE'. 2 record(s) indicate done and evaluable but otherwise missing."
#> attr(,"data")
#>   USUBJID TRTESTCD TRDTC VISIT TRORRES TRSTRESN TRLINKID TRSTAT          RAVE
#> 2       2    LDIAM     2     B       B       NA        2        FORMNAME-R:19
#> 3       3    LDIAM     3     C       C     <NA>        3        FORMNAME-R:19