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 Facult? B-5030 Gembloux (Belgium) T?l : +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
------------------------------------------------------------------------------ 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. ==============================================================================