Andrew,

> What I still don't quite understand is which accuracy values from train() I 
> should trust: those using classProbs=T or classProbs=F?

It depends on whether you need the class probabilities and class
predictions to match (which they would if classProbs = TRUE).

Another option is to use a model where this discrepancy does not exist.

>  train often crashes with 'memory map' errors!)?

I've never seen that. You should describe it more.

Max

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