-
Notifications
You must be signed in to change notification settings - Fork 7
/
check_qs_qsdtc_visit_ordinal_error.R
86 lines (77 loc) · 2.95 KB
/
check_qs_qsdtc_visit_ordinal_error.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
#' @title Check that all QS dates are duplicated or earlier than last
#' visit's (possible datetime data entry error)
#'
#' @description This check identifies QSDTC values that are duplicated or
#' earlier than last visit's. Unscheduled visits are excluded.
#'
#' @param QS SDTM dataset with variables USUBJID, QSCAT, QSORRES, VISITNUM, VISIT, QSDTC
#'
#' @return boolean value if check failed or passed with 'msg' attribute if the
#' test failed
#'
#' @export
#'
#' @author Simon Luo
#'
#' @examples
#'
#' # no case
#' QS1 <- data.frame(USUBJID = c(rep(101, 5), rep(102, 5)),
#' QSCAT = "DLQI",
#' QSDTC = 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),
#' stringsAsFactors = FALSE)
#'
#' QS2 = QS1
#' QS2$QSCAT = "SKINDEX-29"
#'
#' QS <- rbind(QS1, QS2)
#' check_qs_qsdtc_visit_ordinal_error(QS)
#'
#' # adding cases with earlier date
#' QS$QSDTC[QS$USUBJID == 101 & QS$VISIT == "Visit 3"] <- "2017-01-10T08:25"
#' QS$QSDTC[QS$USUBJID == 102 & QS$VISIT == "Visit 2"] <- "2017-01-01T06:25"
#' check_qs_qsdtc_visit_ordinal_error(QS)
#'
#' # adding cases with duplicated date
#' QS$QSDTC[QS$USUBJID == 102 & QS$VISIT == "Visit 3"] <- "2017-01-01T06:25"
#' check_qs_qsdtc_visit_ordinal_error(QS)
#'
check_qs_qsdtc_visit_ordinal_error <- function(QS){
class(QS) <- 'data.frame'
vars = c("USUBJID", "QSCAT", "VISITNUM", "VISIT", "QSDTC")
### First check that required variables exist and return a message if they don't
if (QS %lacks_any% vars) {
fail(lacks_msg(QS, vars))
### Dont run if VISITNUM is all missing
} else if (length(unique(QS[["VISITNUM"]]))<=1) {
fail(msg="VISITNUM exists but only a single value. ")
} else {
mydf2 <- dtc_dupl_early(
dts = subset(QS,!grepl("UNSCHEDU",toupper(QS$VISIT)),),
vars = vars,
### groupby variables used for grouping and visit.order derivation
groupby = vars[c(1, 2)],
dtc = vars[5],
### variables used for ordering before visit.order derivation
vars[1],
vars[2],
vars[3],
vars[4],
vars[5]
)
### Subset if Vis_order not equal Dtc_order
myout <- mydf2[!is.na(mydf2$check.flag), ]
### Print to report
### Return message if no records with QSDTC per VISITNUM
if (nrow(myout) == 0) {
pass()
### Return subset dataframe if there are records with Possible QSDTC data entry error
} else if (nrow(myout) > 0) {
rownames(myout) = NULL
fail(paste("QS has ", nrow(myout), " records with Possible QSDTC data entry error. ", sep = ""), myout)
}
}
}