[R] randomForests predict problem
Torsten Hothorn
Torsten.Hothorn at rzmail.uni-erlangen.de
Wed Apr 2 15:46:05 CEST 2003
On Wed, 2 Apr 2003, Liaw, Andy wrote:
> Yves,
>
> I will add checks for NAs in predict.randomForest().
>
> In the next version of randomForest (currently called 3.9-x), there will be
> facilities for handling NAs in the training set. However, there's no way to
> handle NAs in the test set yet. I believe Leo is still working on that.
>
> In Leo's v.4 of the Fortran code, he uses proximity from random forest to
> iteratively impute NAs, starting with column median or mode (depending on
> variable types). I've implemented this scheme at the R level, so that it
> works for both regression and classification.
>
> There are a couple of things in Leo's new code that I have not added to the
> package, and that's why the version is 3.9 rather than 4.0. If you would
> like to test the new code, please let me know.
yes, sure!
best,
Torsten
>
> Cheers,
> Andy
>
> > -----Original Message-----
> > From: Yves Brostaux [mailto:brostaux.y at fsagx.ac.be]
> > Sent: Wednesday, April 02, 2003 8:34 AM
> > To: r-help at stat.math.ethz.ch
> > Cc: Liaw, Andy; Torsten Hothorn
> > Subject: RE: [R] randomForests predict problem
> >
> >
> > I use randomForest version 3.4-4, but yes, now I correctly
> > omitted NA's it
> > works. I should have made a mistake while removing them first time.
> >
> > I was surprised that this method doesn't have another way to
> > deal with NA's
> > than omitting them. As Torsten Hothorn suggested, the
> > associated predict
> > function should then check for NA's in newdata, shouldn't it ?
> >
> > Thank you both for your answers !
> >
> > At 15:12 02/04/03, Liaw, Andy wrote:
> > >Yves,
> > >
> > >Which version of the package are you using? I get:
> > >
> > > > soy <- na.omit(Soybean)
> > > > ts <- sample(nrow(soy), 150, replace=FALSE)
> > > > sb.rf <- randomForest(Class ~ ., data=soy[-ts,])
> > > > table(predict(sb.rf, soy[ts,], type="class"))
> > >
> > > 2-4-d-injury alternarialeaf-spot
> > > 0 37
> > > anthracnose bacterial-blight
> > > 10 3
> > > bacterial-pustule brown-spot
> > > 2 29
> > > brown-stem-rot charcoal-rot
> > > 11 7
> > > cyst-nematode diaporthe-pod-&-stem-blight
> > > 0 0
> > > diaporthe-stem-canker downy-mildew
> > > 4 8
> > > frog-eye-leaf-spot herbicide-injury
> > > 17 0
> > > phyllosticta-leaf-spot phytophthora-rot
> > > 3 5
> > > powdery-mildew purple-seed-stain
> > > 4 5
> > > rhizoctonia-root-rot
> > > 5
> > >
> > >Cheers,
> > >Andy
> > >
> > > > -----Original Message-----
> > > > From: Yves Brostaux [mailto:brostaux.y at fsagx.ac.be]
> > > > Sent: Wednesday, April 02, 2003 4:46 AM
> > > > To: r-help at stat.math.ethz.ch
> > > > Subject: [R] randomForests predict problem
> > > >
> > > >
> > > > Hello everybody,
> > > >
> > > > I'm testing the randomForest package in order to do some
> > > > simulations and I
> > > > get some trouble with the prediction of new values. The
> > random forest
> > > > computation is fine but each time I try to predict values
> > > > with the newly
> > > > created object, I get an error message. I thought I was
> > > > because NA values
> > > > in the dataframe, but I cleaned them and still got the same
> > > > error. What am
> > > > I doing wrong ?
> > > >
> > > > > library(mlbench)
> > > > > library(randomForest)
> > > > > data(Soybean)
> > > > > test <- sample(1:683, 150, replace=F)
> > > > > sb.rf <- randomForest(Class~., data=Soybean[-test,])
> > > > > sb.rf.pred <- predict(sb.rf, Soybean[test,])
> > > > Error in matrix(t1$countts, nr = nclass, nc = ntest) :
> > > > No data to replace in matrix(...)
> > > >
> > > > I did it the same way with rpart and all worked fine :
> > > > > library(rpart)
> > > > > sb.rp <- rpart(Class~., data=Soybean[-test,])
> > > > > sb.rp.pred <- predict(sb.rp, Soybean[test,], type="class")
> > > >
> > > > Thank you all for any advice you can give to me.
> > > >
> > > > --
> > > > Ir. Yves Brostaux - Statistics and Computer Science Dpt.
> > > > Gembloux Agricultural University
> > > > 8, avenue de la Faculté B-5030 Gembloux (Belgium)
> > > > Tél : +32 (0)81 62 24 69
> > > > E-mail : brostaux.y at fsagx.ac.be
> > > > Web : http://www.fsagx.ac.be/si/
> > > >
> > > > ______________________________________________
> > > > R-help at stat.math.ethz.ch mailing list
> > > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > > >
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