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:[EMAIL PROTECTED] > > Sent: Wednesday, April 02, 2003 8:34 AM > > To: [EMAIL PROTECTED] > > 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:[EMAIL PROTECTED] > > > > Sent: Wednesday, April 02, 2003 4:46 AM > > > > To: [EMAIL PROTECTED] > > > > 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 Facult� B-5030 Gembloux (Belgium) > > > > T�l : +32 (0)81 62 24 69 > > > > E-mail : [EMAIL PROTECTED] > > > > Web : http://www.fsagx.ac.be/si/ > > > > > > > > ______________________________________________ > > > > [EMAIL PROTECTED] mailing list > > > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > > > > > > > > >------------------------------------------------------------- > > ----------------- > > >Notice: This e-mail message, together with any attachments, contains > > >information of Merck & Co., Inc. (Whitehouse Station, New > > Jersey, USA) > > >that may be confidential, proprietary copyrighted and/or legally > > >privileged, and is intended solely for the use of the > > individual or entity > > >named on this message. If you are not the intended > > recipient, and have > > >received this message in error, please immediately return > > this by e-mail > > >and then delete it. > > > > > >============================================================= > > ================= > > > > > > > ------------------------------------------------------------------------------ > Notice: This e-mail message, together with any attachments, contains information of > Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, > proprietary copyrighted and/or legally privileged, and is intended solely for the > use of the individual or entity named on this message. If you are not the intended > recipient, and have received this message in error, please immediately return this > by e-mail and then delete it. > > ============================================================================== > > ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
