Checks for event categories and gives a warning message indicating which level is assumed to be the reference level.
checkArgsEventIndicator(data, event, censored.indicator)a data.frame or data.table containing the source
dataset.
a character string giving the name of the event variable
contained in data. See Details. If event is a numeric
variable, then 0 needs to represent a censored observation, 1 needs to be
the event of interest. Integers 2, 3, ... and so on are treated as
competing events. If event is a factor or character and
censored.indicator is not specified, this function will assume the
reference level is the censored indicator
a character string of length 1 indicating which
value in event is the censored. This function will use
relevel to set censored.indicator as the
reference level. This argument is ignored if the event variable is a
numeric
A list of length two. The first element is the factored event, and the second element is the numeric representation of the event
if (requireNamespace("survival", quietly = TRUE)) {
library(survival) # for veteran data
checkArgsEventIndicator(data = veteran, event = "celltype",
censored.indicator = "smallcell")
checkArgsEventIndicator(data = veteran, event = "status")
}
#> assuming smallcell represents a censored observation and squamous is the event of interest
#> $event.factored
#> [1] event event event event event event event event
#> [9] event censored event event event censored event event
#> [17] event event event event censored censored event event
#> [25] event event event event event event event event
#> [33] event event event event event event event event
#> [41] event event event event event event event event
#> [49] event event event event event event event event
#> [57] event event event event event event event censored
#> [65] event event event event event event event censored
#> [73] censored event event event event event event event
#> [81] event event event event event event event event
#> [89] event event censored event event event event event
#> [97] event event event event event event event event
#> [105] event event event event event censored event event
#> [113] event event event event event event event event
#> [121] event event event event event event event event
#> [129] event event event event event event event event
#> [137] event
#> Levels: censored event
#>
#> $event.numeric
#> [1] 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 0 1
#> [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1
#> [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>
#> $nLevels
#> [1] 2
#>
data("bmtcrr") # from casebase
checkArgsEventIndicator(data = bmtcrr, event = "Sex",
censored.indicator = "M")
#> assuming M represents a censored observation and F is the event of interest
#> $event.factored
#> [1] M F M F F M M F M F M M F M M F M M M M F F M M M M F M M F M M F M F M M
#> [38] M F F M M F M M M M M M M F F F F M F F M F M F M M F M F F M F M M M F F
#> [75] M M F M M F M F M F F M F M M M F F M M F F M M F F F F F M M F F M F M M
#> [112] M F M F M F M M M M F F M M F M M F M F M F M M M M F M M F M F F F M M M
#> [149] F F M F M F M M M F F M F F M F F M F M M F F M M F M F M
#> Levels: M F
#>
#> $event.numeric
#> [1] 0 1 0 1 1 0 0 1 0 1 0 0 1 0 0 1 0 0 0 0 1 1 0 0 0 0 1 0 0 1 0 0 1 0 1 0 0
#> [38] 0 1 1 0 0 1 0 0 0 0 0 0 0 1 1 1 1 0 1 1 0 1 0 1 0 0 1 0 1 1 0 1 0 0 0 1 1
#> [75] 0 0 1 0 0 1 0 1 0 1 1 0 1 0 0 0 1 1 0 0 1 1 0 0 1 1 1 1 1 0 0 1 1 0 1 0 0
#> [112] 0 1 0 1 0 1 0 0 0 0 1 1 0 0 1 0 0 1 0 1 0 1 0 0 0 0 1 0 0 1 0 1 1 1 0 0 0
#> [149] 1 1 0 1 0 1 0 0 0 1 1 0 1 1 0 1 1 0 1 0 0 1 1 0 0 1 0 1 0
#>
#> $nLevels
#> [1] 2
#>
checkArgsEventIndicator(data = bmtcrr, event = "D",
censored.indicator = "AML")
#> assuming AML represents a censored observation and ALL is the event of interest
#> $event.factored
#> [1] ALL AML ALL ALL ALL ALL ALL ALL ALL ALL ALL AML AML ALL ALL ALL ALL AML
#> [19] ALL AML ALL ALL ALL ALL AML ALL ALL AML ALL AML AML AML ALL ALL ALL AML
#> [37] ALL AML AML ALL AML AML AML AML AML AML ALL AML AML AML AML AML AML ALL
#> [55] ALL AML ALL AML AML ALL AML ALL AML AML AML AML AML ALL ALL ALL ALL AML
#> [73] ALL ALL ALL AML AML AML AML ALL AML AML ALL AML ALL AML AML ALL AML AML
#> [91] AML AML AML AML AML ALL AML ALL ALL ALL AML ALL AML AML ALL AML AML AML
#> [109] AML AML AML AML AML AML AML ALL AML AML ALL ALL ALL AML ALL ALL ALL ALL
#> [127] AML AML AML ALL AML AML AML AML ALL AML AML AML ALL AML AML AML AML ALL
#> [145] AML ALL ALL AML ALL AML ALL AML AML AML AML AML ALL ALL AML AML ALL AML
#> [163] AML AML ALL AML ALL ALL ALL AML AML AML AML AML AML AML AML
#> Levels: AML ALL
#>
#> $event.numeric
#> [1] 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 1 0 1 1 1 1 0 1 1 0 1 0 0 0 1 1 1 0 1
#> [38] 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1 0 0 1 0 1 0 0 0 0 0 1 1 1 1 0 1 1
#> [75] 1 0 0 0 0 1 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 1 0 1 1 1 0 1 0 0 1 0 0 0 0 0 0
#> [112] 0 0 0 0 1 0 0 1 1 1 0 1 1 1 1 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 0
#> [149] 1 0 1 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0
#>
#> $nLevels
#> [1] 2
#>
checkArgsEventIndicator(data = bmtcrr, event = "Status")
#> $event.factored
#> [1] competing event event censored competing event
#> [5] competing event competing event censored competing event
#> [9] censored event competing event competing event
#> [13] competing event event competing event competing event
#> [17] censored competing event competing event competing event
#> [21] event competing event event event
#> [25] competing event event event censored
#> [29] event censored event censored
#> [33] competing event censored event competing event
#> [37] event censored competing event competing event
#> [41] competing event competing event competing event competing event
#> [45] event censored event event
#> [49] competing event competing event censored competing event
#> [53] competing event competing event censored censored
#> [57] competing event event competing event event
#> [61] competing event competing event competing event censored
#> [65] censored event competing event event
#> [69] competing event censored censored censored
#> [73] competing event event event censored
#> [77] event event censored competing event
#> [81] event event competing event censored
#> [85] event censored censored censored
#> [89] competing event event event competing event
#> [93] competing event censored competing event event
#> [97] competing event event competing event censored
#> [101] event censored competing event censored
#> [105] competing event event censored event
#> [109] competing event censored competing event competing event
#> [113] competing event competing event competing event event
#> [117] competing event event competing event competing event
#> [121] censored censored event event
#> [125] event competing event competing event competing event
#> [129] censored competing event competing event competing event
#> [133] event censored censored censored
#> [137] event competing event event event
#> [141] censored event competing event censored
#> [145] event competing event event event
#> [149] event event censored event
#> [153] competing event competing event competing event competing event
#> [157] event event competing event competing event
#> [161] competing event competing event competing event competing event
#> [165] censored censored censored competing event
#> [169] event censored event event
#> [173] censored event censored censored
#> [177] event
#> Levels: censored event competing event
#>
#> $event.numeric
#> [1] 2 1 0 2 2 2 0 2 0 1 2 2 2 1 2 2 0 2 2 2 1 2 1 1 2 1 1 0 1 0 1 0 2 0 1 2 1
#> [38] 0 2 2 2 2 2 2 1 0 1 1 2 2 0 2 2 2 0 0 2 1 2 1 2 2 2 0 0 1 2 1 2 0 0 0 2 1
#> [75] 1 0 1 1 0 2 1 1 2 0 1 0 0 0 2 1 1 2 2 0 2 1 2 1 2 0 1 0 2 0 2 1 0 1 2 0 2
#> [112] 2 2 2 2 1 2 1 2 2 0 0 1 1 1 2 2 2 0 2 2 2 1 0 0 0 1 2 1 1 0 1 2 0 1 2 1 1
#> [149] 1 1 0 1 2 2 2 2 1 1 2 2 2 2 2 2 0 0 0 2 1 0 1 1 0 1 0 0 1
#>
#> $nLevels
#> [1] 3
#>