argument recode.target of getTaskData is not consistent with the documentation

[HerrMo]

Hi,

in the docu of getTaskData it says under recode.target: "For survival, you may choose to recode the survival times to 'left', 'right' or 'interval2' censored times using 'lcens', 'rcens' or 'icens', respectively."
This is not consistent with the implementation. If one of these options is chosen, e.g.recode.target = "rcens", an error occurs. Instead, recode.traget = "surv" works. See example:

library(mlr)
library(prodlim)

X <- cbind(matrix(nrow=40, ncol=40, data=rnorm(40*40)),
           matrix(nrow=40, ncol=30, data=rnorm(40*30, mean=1, sd=2)),
           matrix(nrow=40, ncol=100, data=rnorm(40*100, mean=2, sd=3)))
colnames(X) <- paste0("X", 1:dim(X)[2])

ysurv <- prodlim::SimSurv(40)[, c(3,7)]

df_data <- cbind(ysurv, X)
task <- makeSurvTask(id = "exampletask", data = df_data, target = c("time", "status"))

# does not work
tt <- getTaskData(task, target.extra = TRUE, recode.target = "icens")

# works
tt <- getTaskData(task, target.extra = TRUE, recode.target = "surv")

As far as I understand that, the options listed in the docu are simply not implemented.
If you look at the source code, you will see that.

mlr/R/Task_operators.R

Lines 333 to 335 in 1a2d34b

	if (recode.target %nin% c("no", "surv")) {
	res[, tn] = recodeY(res[, tn], type = recode.target, task$task.desc)
	}

mlr/R/Task_operators.R

Lines 340 to 354 in 1a2d34b

	recodeY = function(y, type, td) {
	if (type == "no")
	return(y)
	if (type == "drop.levels")
	return(factor(y))
	if (type == "01")
	return(as.numeric(y == td$positive))
	if (type == "-1+1")
	return(as.numeric(2L * (y == td$positive) - 1L))
	if (type == "surv")
	return(Surv(y[, 1L], y[, 2L], type = "right"))
	if (type == "multilabel.factor")
	return(lapply(y, function(x) factor(x, levels = c("TRUE", "FALSE"))))
	stopf("Unknown value for 'type': %s", type)
	}

Kind regards

[pat-s]

Thanks, looks like the doc is not up to date then.

[pat-s]

I've taken a look but couldn't find the commit that changed the implementation. I just found that there were valid options for 'lcens', 'rcens' or 'icens' in the package at some point.

Could you explain shortly what the current option "surv" does? I cannot infer that by just looking at the example and the transformation.

[HerrMo]

Many methods require an object of class Surv (s. survival::Surv). Option "surv" changes the target into such a Surv-object with censoring being set to right censoring (most standard censoring type) via type = "right"

mlr/R/Task_operators.R

Line 350 in 1a2d34b

return(Surv(y[, 1L], y[, 2L], type = "right"))

Otherwise you would get as target a data.frame with the survival times in the fist column and the censoring indicators in the second.

[stale]

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