test.join aggregation does not join probabilities

[berndbischl]

task = sonar.task
lrn = makeLearner("classif.rpart", predict.type = "prob")

rin = makeResampleDesc("Holdout")
mm = setAggregation(auc, test.join)
r = resample(lrn, task, rin, measures = mm)

This leads to Error in getPredictionProbabilities(pred, cl = levs) : Trying to get probabilities for nonexistant classes: M,R

It is also obvious from the source code. NB: we have potentially more columns we need to join like se and the stuff from survival...

@mllg as you pushed this some time ago

[larskotthoff]

Did the PR solve this completely or should we leave this open?

[giuseppec]

The part

NB: we have potentially more columns we need to join like se and the stuff from survival...

was not addressed in the PR, therefore we could leave this open.

[jakob-r]

This error still prevails

task = wpbc.task
lrn = makeLearner("surv.rpart")
rin = makeResampleDesc("Holdout")
mm = setAggregation(cindex, test.join)
r = resample(lrn, task, rin, measures = mm)
#[Resample] holdout iter: 1
#Error in FUN(X[[i]], ...) : 
#  You need to have 'truth.time' and 'truth.event' columns in your pred object for measure cindex!

[jakob-r]

And

task = yeast.task
lrn = makeLearner("multilabel.cforest")
rin = makeResampleDesc("Holdout")
mm = setAggregation(multilabel.acc, test.join)
r = resample(lrn, task, rin, measures = mm)
#[Resample] holdout iter: 1
#Error in `row.names<-.data.frame`(`*tmp*`, value = value) : 
#  invalid 'row.names' length

[jakob-r]

In other words: We should not write custom code for every task class in test.join but find a generalized solution.

[pat-s]

library(mlr)
#> Loading required package: ParamHelpers

task = wpbc.task
lrn = makeLearner("surv.rpart")
rin = makeResampleDesc("Holdout")
mm = setAggregation(cindex, test.join)
r = resample(lrn, task, rin, measures = mm)
#> Resampling: holdout
#> Measures:             cindex
#> [Resample] iter 1:    0.6156373
#> Error in FUN(X[[i]], ...): You need to have 'truth.time' and 'truth.event' columns in your pred object for measure cindex!

^{Created on 2019-12-31 by the reprex package (v0.3.0)}