[R] Different results from random.Forest with test option and using predict function

[Peter Langfelder]

On Mon, Dec 3, 2012 at 3:30 PM, tdbuskirk <Trent.Buskirk at nielsen.com> wrote:
>
> Hello R Gurus,
>
> I am perplexed by the different results I obtained when I ran code like
> this:
> set.seed(100)
> test1<-randomForest(BinaryY~., data=Xvars, trees=51, mtry=5, seed=200)
> predict(test1, newdata=cbind(NewBinaryY, NewXs), type="response")
>

Not sure about this since I haven't used predict.randomForest
extensively, but newdata usually contains predictors only, not the
response. Try using newdata = NexXs.

HTH,

Peter

> and this code:
> set.seed(100)
> test2<-randomForest(BinaryY~., data=Xvars, trees=51, mtry=5, seed=200,
> xtest=NewXs, ytest=NewBinarY)
>
> The confusion matrices for the two forests I thought would be the same by
> virtue of the same seed settings, but they differ as do the predicted
> values
> as well as the votes.  At first I thought it was just the way ties were
> broken, so I changed the number of trees to an odd number so there are no
> ties anymore.
>
> Can anyone shed light on what I am hoping is a simple oversight?  I just
> can't figure out why the results of the predictions from these two forests
> applied to the NewBinaryYs and NewX data sets would not be the same.
>
> Thanks for any hints and help.
>
> Sincerely,
>
> Trent Buskirk
>
>
>
> --
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