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/

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

Well, thank you for your answer, but this is not doing the right thing,
that is predicting the Class value for the test set Soybean[test,]. It
gives instead prediction for data used for forest computation (ignoring all
data with NA's) ; 'data' argument is simply ignored as the right name for
this argument is 'newdata', which still gives the same error when named.

 > length(sb.rf.pred)

[1] 445

 > dim(Soybean[test,])

[1] 150  36

 > dim(Soybean[-test,])

[1] 533  36

 > sb.rf.pred <- predict(sb.rf, newdata=st)

Error in matrix(t1$countts, nr = nclass, nc = ntest) :
         No data to replace in matrix(...)

At 13:13 02/04/03, you wrote:

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