R/check_pr_prlat.R
check_pr_prlat.Rd
This check assesses observations where PRCAT contains the word OCULAR and flags records with missing/inconsistent laterality
check_pr_prlat(PR, preproc = identity, ...)
Procedure/Surgery Dataset for Ophtho Study with variables USUBJID, PRCAT, PRLAT, PRTRT, PROCCUR, PRPRESP, PRSPID (if Present), PRSTDTC (if Present), PRINDC (if Present)
An optional company specific preprocessing script
Other arguments passed to methods
PR <- data.frame(
USUBJID = 1:5,
PRCAT = "PRIOR OCULAR SURGERIES AND PROCEDURES",
PRSTDTC = 1:5,
PRLAT = c("Left", "","Bilateral", "", ""),
PRTRT = c("A", "B", "A", "B", "A"),
PROCCUR = c("Y", "N", "N", "Y", "Y"),
PRPRESP = "Y",
PRSPID = "FORMNAME-R:2/L:2XXXX",
stringsAsFactors = FALSE)
check_pr_prlat(PR,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 record(s) with PRLAT Missing from records with PRCAT containing the word OCULAR when expected to be populated. "
#> attr(,"data")
#> USUBJID PRCAT PRSTDTC RAVE PRLAT
#> 1 4 PRIOR OCULAR SURGERIES AND PROCEDURES 4 FORMNAME-R:2
#> 2 5 PRIOR OCULAR SURGERIES AND PROCEDURES 5 FORMNAME-R:2
#> PRTRT
#> 1 B
#> 2 A
PR <- data.frame(
USUBJID = 1:5,
PRCAT = "CONCURRENT OCULAR PROCEDURE",
PRSTDTC = 1:5,
PRLAT = c("Left", "LEFT","Bilateral", "RIGHT", "RIgHT"),
PRTRT = c("A", "B", "A", "B", "A"),
PROCCUR = NA,
PRPRESP = NA,
stringsAsFactors = FALSE)
check_pr_prlat(PR)
#> [1] TRUE
PR <- data.frame(
USUBJID = 1:5,
PRCAT = "CONCURRENT OCULAR PROCEDURE",
PRSTDTC = 1:5,
PRLAT = c("Left", "LEFT","Bilateral", "RIGHT", ""),
PRTRT = c("A", "B", "A", "B", "A"),
PROCCUR = NA,
PRPRESP = NA,
stringsAsFactors = FALSE)
check_pr_prlat(PR)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 record(s) with PRLAT Missing from records with PRCAT containing the word OCULAR when expected to be populated. "
#> attr(,"data")
#> USUBJID PRCAT PRSTDTC PRLAT PRTRT
#> 1 5 CONCURRENT OCULAR PROCEDURE 5 A
PR <- data.frame(
USUBJID = 1:5,
PRCAT = "CONCURRENT OCULAR PROCEDURE",
PRSTDTC = 1:5,
PRLAT = c("Left", "","Bilateral", "RIGHT", ""),
PRTRT = c("A", "B", "A", "B", "A"),
PROCCUR = c("Y", "N", "N", "Y", "Y"),
PRPRESP = "Y",
stringsAsFactors = FALSE)
check_pr_prlat(PR)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 record(s) with PRLAT Missing from records with PRCAT containing the word OCULAR when expected to be populated. "
#> attr(,"data")
#> USUBJID PRCAT PRSTDTC PRLAT PRTRT
#> 1 5 CONCURRENT OCULAR PROCEDURE 5 A
PR <- data.frame(
USUBJID = 1:5,
PRCAT = c(rep("CONCURRENT NON-OCULAR PROCEDURE",3),rep("CONCURRENT OCULAR PROCEDURE",2)),
PRSTDTC = 1:5,
PRLAT = c("", "","", "RIGHT", ""),
PRTRT = c("A", "B", "A", "B", "A"),
PROCCUR = c("Y", "N", "N", "Y", "Y"),
PRPRESP = "Y",
stringsAsFactors = FALSE)
check_pr_prlat(PR)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 record(s) with PRLAT Missing from records with PRCAT containing the word OCULAR when expected to be populated. "
#> attr(,"data")
#> USUBJID PRCAT PRSTDTC PRLAT PRTRT
#> 1 5 CONCURRENT OCULAR PROCEDURE 5 A