randomForests predict problem

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

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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 !
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

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