R/check_cm_cmlat.R
check_cm_cmlat.Rd
This check assesses CMCAT = "CONCOMITANT MEDICATIONS" and flags potential ocular records with missing/inconsistent route and laterality: for eye-related CMROUTE ('INTRAVITREAL', 'OPHTHALMIC', etc.), CMLAT is not populated -or- CMROUTE is not eye-related (i.e., not INTRAVITREAL, OPHTHALMIC, TOPICAL, etc.) but CMLAT is LEFT/RIGHT/BILATERAL.
check_cm_cmlat(CM, preproc = identity, ...)
Concomitant Medications Dataset for Ophtho Study with variables USUBJID, CMCAT, CMLAT, CMDECOD, CMTRT, CMROUTE, CMSPID (if Present), CMSTDTC (if Present)
An optional company specific preprocessing script
Other arguments passed to methods
CM <- data.frame(
USUBJID = 1:7,
CMCAT = "CONCOMITANT MEDICATIONS",
CMSTDTC = 1:7,
CMLAT = c("Left", "","Bilateral", "", "", "LEFT", ""),
CMTRT = c("A", "B", "A", "B", "A", "A", "B"),
CMDECOD = c("A", "B", "A", "B", "A", "A", "B"),
CMROUTE = c("","OPHTHALMIC","INTRAVITREAL","INTRAVITREAL",
"opHTHALMIC", "INTRaOCULAr", "INTRaOCULAr"),
CMSPID = "FORMNAME-R:13/L:13XXXX",
stringsAsFactors = FALSE)
check_cm_cmlat(CM,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "5 record(s) with CMLAT Missing when CM is Eye related, or CMLAT is LEFT/RIGHT/BILATERAL and CMROUTE is not Eye related."
#> attr(,"data")
#> USUBJID CMSTDTC RAVE CMLAT CMTRT CMDECOD CMROUTE
#> 1 1 1 FORMNAME-R:13 Left A A
#> 2 2 2 FORMNAME-R:13 B B OPHTHALMIC
#> 3 4 4 FORMNAME-R:13 B B INTRAVITREAL
#> 4 5 5 FORMNAME-R:13 A A opHTHALMIC
#> 5 7 7 FORMNAME-R:13 B B INTRaOCULAr
CM <- data.frame(
USUBJID = 1:5,
CMCAT = rep("CONCOMITANT MEDICATIONS",5),
CMSTDTC = 1:5,
CMLAT = c("Left", "LEFT","Bilateral",
"RIGHT", "RIgHT"),
CMTRT = c("A", "B", "A", "B", "A"),
CMDECOD = c("A", "B", "A", "B", "A"),
CMROUTE = c("","OPHTHALMIC","INTRAVITREAL",
"INTRaOCULAr", "opHTHALMIC"),
stringsAsFactors = FALSE)
check_cm_cmlat(CM)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 record(s) with CMLAT Missing when CM is Eye related, or CMLAT is LEFT/RIGHT/BILATERAL and CMROUTE is not Eye related."
#> attr(,"data")
#> USUBJID CMSTDTC CMLAT CMTRT CMDECOD CMROUTE
#> 1 1 1 Left A A
CM <- data.frame(
USUBJID = 1:5,
CMCAT = "CONCOMITANT MEDICATIONS",
CMSTDTC = 1:5,
CMLAT = c("Left", "LEFT","Bilateral", "RIGHT", "RIgHT"),
CMTRT = c("A", "B", "A", "B", "A"),
CMDECOD = c("A", "B", "A", "B", "A"),
#CMROUTE = c("","OPHTHALMIC","INTRAVITREAL","INTRaOCULAr", "opHTHALMIC"),
stringsAsFactors = FALSE)
check_cm_cmlat(CM)
#> [1] FALSE
#> attr(,"msg")
#> [1] "CM is missing the variable: CMROUTE"