[R] randomForests predict problem

[Torsten Hothorn]

> 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(...)


try

R> test <- sample(1:683, 150, replace=FALSE)
R>
R> st <- Soybean[test,]
R>
R> sb.rf <- randomForest(Class~., data=Soybean, subset=-test)
R> sb.rf.pred <- predict(sb.rf, data=st)
R>
R> sb.rf.pred[1:10]
 [1] diaporthe-stem-canker diaporthe-stem-canker diaporthe-stem-canker
 [4] diaporthe-stem-canker diaporthe-stem-canker diaporthe-stem-canker
 [7] diaporthe-stem-canker charcoal-rot          charcoal-rot
[10] charcoal-rot
19 Levels: 2-4-d-injury alternarialeaf-spot anthracnose ...
rhizoctonia-root-rot


Torsten

>
> 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/
>
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