Checks for event categories and gives a warning message indicating which level is assumed to be the reference level.

checkArgsEventIndicator(data, event, censored.indicator)

Arguments

data

a data.frame or data.table containing the source dataset.

event

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

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

Value

A list of length two. The first element is the factored event, and the second element is the numeric representation of the event

Examples

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 #>