#' @rdname Task
#' @param censoring [\code{character(1)}]\cr
#' Censoring type. Allowed choices are \dQuote{rcens} for right censored data (default),
#' \dQuote{lcens} for left censored and \dQuote{icens} for interval censored data using
#' the \dQuote{interval2} format.
#' See \code{\link[survival]{Surv}} for details.
#' @export
makeSurvTask = function(id = deparse(substitute(data)), data, target, censoring = "rcens", weights = NULL, blocking = NULL, fixup.data = "warn", check.data = TRUE) {
assertString(id)
assertDataFrame(data)
assertCharacter(target, any.missing = FALSE, len = 2L)
assertChoice(censoring, choices = c("rcens", "lcens", "icens"))
assertChoice(fixup.data, choices = c("no", "quiet", "warn"))
assertFlag(check.data)
if (fixup.data != "no") {
if (censoring %in% c("lcens", "rcens")) {
time = data[[target[1L]]]
event = data[[target[2L]]]
if (is.integer(time)) {
data[[target[1L]]] = as.double(time)
}
if (is.numeric(event)) {
if (testIntegerish(event) && all(as.integer(event) %in% c(0L, 1L)))
data[[target[2L]]] = (as.integer(event) == 1L)
} else if (is.factor(event)) {
lvls = levels(event)
if (length(lvls) == 2L) {
if (all(lvls %in% c("TRUE", "FALSE"))) {
data[[target[2L]]] = (event == "TRUE")
} else if (all(lvls %in% c("0", "1"))) {
data[[target[2L]]] = (as.character(event) == "1")
}
}
}
} else { # icens
time1 = data[[target[1L]]]
time2 = data[[target[2L]]]
if (is.integer(time1))
data[[target[1L]]] = as.numeric(time1)
if (is.integer(time2))
data[[target[2L]]] = as.numeric(time2)
}
}
task = makeSupervisedTask("regr", data, target, weights, blocking, fixup.data = fixup.data, check.data = check.data)
if (check.data) {
if (censoring %in% c("lcens", "rcens")) {
time = data[[target[1L]]]
event = data[[target[2L]]]
assertNumeric(time, lower = 0, finite = TRUE, any.missing = FALSE, .var.name = "target column time")
assertLogical(event, any.missing = FALSE, .var.name = "target column event")
} else { # icens
time1 = data[[target[1L]]]
time2 = data[[target[2L]]]
assertNumeric(time1, any.missing = TRUE, finite = FALSE, .var.name = "target column time1")
assertNumeric(time2, any.missing = TRUE, finite = FALSE, .var.name = "target column time2")
}
}
task$task.desc = makeSurvTaskDesc(id, data, target, weights, blocking, censoring)
addClasses(task, "SurvTask")
}
makeSurvTaskDesc = function(id, data, target, weights, blocking, censoring) {
td = makeTaskDescInternal("surv", id, data, target, weights, blocking)
td$censoring = censoring
addClasses(td, c("SurvTaskDesc", "SupervisedTaskDesc"))
}
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